Contacts of the helix formed by residues 629 - 654 (chain A) in PDB entry 4PE5
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ALA 629 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
577A LEU* 4.4 20.3 - - + +
580A LEU* 3.8 19.3 - - + -
626A SER 3.8 4.0 - - - +
627A PHE* 3.0 11.2 + - + +
628A SER* 1.3 80.8 - - - +
630A ARG* 1.3 60.7 + - - +
631A ILE* 3.2 4.0 - - - +
632A LEU* 3.3 15.9 + - + +
633A GLY* 3.1 22.2 + - - -
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Residues in contact with ARG 630 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
626A SER* 3.2 30.3 + - - +
628A SER* 3.8 1.2 - - - +
629A ALA* 1.3 76.8 - - - +
631A ILE* 1.3 60.8 + - - +
633A GLY* 3.2 3.1 + - - +
634A MET* 2.9 26.5 + - - +
607B TRP* 5.9 7.6 - - + -
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Residues in contact with ILE 631 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
628A SER 6.5 0.2 - - - -
629A ALA* 3.2 1.3 - - - +
630A ARG* 1.3 76.9 - - - +
632A LEU* 1.3 60.2 + - - +
634A MET* 3.2 8.7 + - - +
635A VAL* 2.9 27.9 + - - +
835B THR* 6.0 5.6 - - - -
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Residues in contact with LEU 632 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
576A MET* 6.5 0.7 - - + -
577A LEU* 6.2 2.7 - - + -
629A ALA* 3.3 20.1 + - + +
631A ILE* 1.3 78.3 - - - +
633A GLY* 1.3 57.5 + - - +
635A VAL* 3.5 8.3 + - - +
636A TRP* 2.9 27.5 + - - +
828B ALA* 5.7 4.5 - - + +
832B SER* 4.9 17.7 - - - -
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Residues in contact with GLY 633 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
613A VAL* 5.7 1.9 - - - +
629A ALA 3.1 13.9 + - - -
630A ARG* 3.2 5.4 + - - -
631A ILE 3.2 0.2 - - - -
632A LEU* 1.3 75.8 - - - +
634A MET* 1.3 58.7 + - - +
636A TRP* 3.4 8.0 + - - +
637A ALA* 2.9 27.0 + - - +
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Residues in contact with MET 634 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
630A ARG 2.9 12.8 + - - +
631A ILE* 3.2 12.5 + - - +
633A GLY* 1.3 75.8 - - - +
635A VAL* 1.3 59.7 + - - +
637A ALA* 3.2 8.8 + - - +
638A GLY* 2.9 23.6 + - - -
607B TRP* 6.6 0.2 - - - -
610B TRP* 5.5 11.9 - - + -
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Residues in contact with VAL 635 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
631A ILE 2.9 15.2 + - - +
632A LEU* 3.7 7.4 - - - +
634A MET* 1.3 74.7 - - - +
636A TRP* 1.3 59.4 + - - +
638A GLY* 3.2 2.7 + - - -
639A PHE* 2.9 27.5 + - - +
825B LEU* 5.8 3.5 - - + +
828B ALA* 3.7 30.3 - - + -
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Residues in contact with TRP 636 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
573A VAL* 5.4 13.2 - - + -
613A VAL* 5.4 6.2 - - + +
632A LEU 2.9 18.8 + - - +
633A GLY* 3.6 9.6 - - - +
635A VAL* 1.3 76.4 - - - +
637A ALA* 1.3 59.5 + - - +
639A PHE* 3.5 7.4 + - - +
640A ALA* 2.9 28.1 + - - +
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Residues in contact with ALA 637 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
613A VAL* 5.1 12.1 - - + +
633A GLY 2.9 18.1 + - - +
634A MET* 3.4 9.9 - - - +
635A VAL 3.2 0.2 - - - -
636A TRP* 1.3 75.7 - - - +
638A GLY* 1.3 59.2 + - - +
640A ALA* 3.6 7.2 - - - +
641A MET* 2.9 29.5 + - - +
611B GLY* 6.4 2.5 - - - -
614B PHE* 4.4 15.9 - - + +
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Residues in contact with GLY 638 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
634A MET 2.9 13.9 + - - -
635A VAL* 3.2 5.1 + - - -
637A ALA* 1.3 77.6 - - - +
639A PHE* 1.3 55.7 + - - +
641A MET* 3.4 6.5 + - - +
642A ILE* 2.9 29.3 + - - +
614B PHE* 5.9 0.9 - - - -
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Residues in contact with PHE 639 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
635A VAL 2.9 16.3 + - - +
636A TRP* 3.8 7.2 - - - +
638A GLY* 1.3 75.7 - - - +
640A ALA* 1.3 58.7 + - - +
642A ILE* 3.5 6.8 + - - +
643A ILE* 2.9 28.2 + - - +
821B VAL 5.4 5.2 - - - +
825B LEU* 4.9 17.7 - - + -
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Residues in contact with ALA 640 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
613A VAL* 3.8 27.1 - - + +
614A LEU* 4.4 10.4 - - + +
636A TRP 2.9 18.0 + - - +
637A ALA* 3.6 8.3 - - - +
639A PHE* 1.3 75.8 - - - +
641A MET* 1.3 61.0 + - - +
643A ILE* 3.3 7.1 + - - +
644A VAL* 2.9 29.1 + - - +
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Residues in contact with MET 641 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
637A ALA 2.9 17.6 + - - +
638A GLY* 3.8 7.2 - - - +
640A ALA* 1.3 75.8 - - - +
642A ILE* 1.3 58.1 + - - +
644A VAL* 3.4 7.1 + - - +
645A ALA* 2.9 29.8 + - - +
614B PHE* 4.3 20.0 - - + -
615B ASN* 5.5 2.0 - - + +
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Residues in contact with ILE 642 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
638A GLY 2.9 17.7 + - - +
639A PHE* 3.8 8.5 - - - +
641A MET* 1.3 74.6 - - - +
643A ILE* 1.3 58.8 + - - +
645A ALA* 3.9 6.1 - - - +
646A SER* 2.9 31.4 + - - -
551B LEU 6.4 0.4 - - - +
821B VAL* 5.7 10.3 - - + -
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Residues in contact with ILE 643 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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566A VAL* 6.4 2.0 - - + -
639A PHE 2.9 18.8 + - - +
640A ALA* 3.5 8.7 - - - +
641A MET 3.3 0.2 - - - -
642A ILE* 1.3 75.7 - - - +
644A VAL* 1.3 59.7 + - - +
646A SER* 3.5 5.4 + - - -
647A TYR* 2.9 30.5 + - - +
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Residues in contact with VAL 644 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
640A ALA 2.9 16.8 + - - +
641A MET* 3.7 7.2 - - - +
643A ILE* 1.3 75.1 - - - +
645A ALA* 1.3 60.5 + - - +
647A TYR* 3.4 5.5 + - - +
648A THR* 2.9 30.8 + - - -
644D ALA* 5.6 1.4 - - - +
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Residues in contact with ALA 645 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
641A MET 2.9 18.2 + - - +
642A ILE* 3.9 6.5 - - - +
644A VAL* 1.3 77.3 - - - +
646A SER* 1.3 58.4 + - - +
648A THR* 3.5 3.3 + - - -
649A ALA* 2.9 30.7 + - - +
646B TYR* 4.1 23.8 - - + +
647B THR* 4.3 18.6 - - - +
650B LEU* 4.7 4.4 - - + +
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Residues in contact with SER 646 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
642A ILE 2.9 19.9 + - - -
643A ILE* 3.8 5.6 - - - -
645A ALA* 1.3 73.3 - - - +
647A TYR* 1.3 60.1 + - - +
649A ALA* 3.9 6.0 - - - +
650A ASN* 2.9 31.9 + - - +
650B LEU* 5.9 0.9 - - - -
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Residues in contact with TYR 647 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
557A PRO* 5.9 1.9 - - - +
643A ILE 2.9 19.1 + - - +
644A VAL* 3.7 6.5 - - - +
646A SER* 1.3 78.8 - - - +
648A THR* 1.3 56.8 + - - +
650A ASN* 3.5 4.7 + - - +
651A LEU* 2.9 30.4 + - - +
644D ALA* 5.4 6.7 - - + -
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Residues in contact with THR 648 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
644A VAL 2.9 18.1 + - - -
645A ALA* 3.8 4.3 - - - -
647A TYR* 1.3 75.6 - - - +
649A ALA* 1.3 59.8 + - - +
651A LEU* 3.3 6.6 + - - +
652A ALA* 2.9 28.8 + - - +
647B THR* 3.9 20.9 - - - -
644D ALA* 4.6 23.5 - - - +
647D THR* 5.5 6.1 - - - -
648D ALA* 4.0 4.3 - - - +
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Residues in contact with ALA 649 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
645A ALA 2.9 18.6 + - - +
646A SER* 3.9 5.4 - - - +
648A THR* 1.3 76.1 - - - +
650A ASN* 1.3 57.8 + - - +
652A ALA* 3.2 6.9 + - - +
653A ALA* 2.9 29.2 + - - +
647B THR* 4.5 5.1 - - + +
650B LEU* 3.9 26.2 - - + +
651B ALA* 3.9 19.3 - - - +
654B MET* 4.9 5.5 - - + +
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Residues in contact with ASN 650 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
557A PRO* 3.6 31.6 - - + +
646A SER 2.9 20.3 + - - +
647A TYR* 3.9 4.9 - - - +
649A ALA* 1.3 75.8 - - - +
651A LEU* 1.3 58.0 + - - +
653A ALA* 3.9 7.1 - - - +
654A PHE* 3.0 30.7 + - - +
654B MET* 6.1 0.7 - - - -
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Residues in contact with LEU 651 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
557A PRO* 5.7 2.0 - - - +
647A TYR 2.9 19.7 + - - +
648A THR* 3.6 7.6 - - - +
649A ALA 3.2 0.4 - - - -
650A ASN* 1.3 77.2 - - - +
652A ALA* 1.3 60.0 + - - +
653A ALA 3.3 0.2 - - - -
654A PHE* 3.9 6.1 + - - +
655A LEU* 3.4 19.8 - - - +
644D ALA* 4.7 7.9 - - + +
645D SER* 5.6 1.8 - - - -
648D ALA* 3.6 17.3 - - + +
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Residues in contact with ALA 652 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
648A THR 2.9 16.7 + - - +
649A ALA* 3.7 7.6 - - - +
650A ASN 3.2 0.2 - - - -
651A LEU* 1.3 76.5 - - - +
653A ALA* 1.3 61.8 + - - +
654A PHE 3.5 0.2 - - - -
655A LEU* 4.1 1.9 - - - +
656A VAL* 3.4 26.0 + - - +
651B ALA* 4.7 13.5 - - + -
648D ALA* 3.7 25.4 - - + +
651D ALA* 4.5 11.4 - - + -
652D ALA* 5.3 0.5 - - - +
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Residues in contact with ALA 653 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
649A ALA 2.9 16.5 + - - +
650A ASN* 3.9 8.5 - - - +
651A LEU 3.3 0.2 - - - -
652A ALA* 1.3 77.2 - - - +
654A PHE* 1.3 56.1 + - - +
655A LEU 3.1 9.0 + - - -
656A VAL* 4.0 11.2 + - - -
651B ALA* 5.8 1.3 - - + +
654B MET* 4.5 20.9 - - + +
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Residues in contact with PHE 654 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
550A THR* 3.5 22.0 - - - +
557A PRO* 6.1 4.3 - - + -
650A ASN 3.0 17.7 + - - +
651A LEU* 3.9 5.5 + - - +
653A ALA* 1.3 74.8 - - - +
655A LEU* 1.3 59.9 + - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il