Contacts of the helix formed by residues 631 - 654 (chain D) 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 MET 631 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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824A ILE* 5.2 19.9 - - + +
827A GLY* 5.5 10.8 - - - -
828A ILE* 5.7 0.7 - - - +
630D ILE* 1.3 78.3 - - - +
632D VAL* 1.3 62.2 + - - +
633D SER 3.2 3.3 + - - -
634D VAL* 3.5 17.4 + - + +
635D TRP* 3.7 7.8 + - - +
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Residues in contact with VAL 632 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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612D LEU* 5.7 1.9 - - - +
630D ILE* 3.5 2.3 - - - -
631D MET* 1.3 77.7 - - - +
633D SER* 1.3 59.1 + - - +
634D VAL 3.3 0.4 - - - -
635D TRP* 3.2 11.5 + - + +
636D ALA* 2.9 26.9 + - - +
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Residues in contact with SER 633 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
611A TRP* 4.9 23.6 - - - -
612A GLY* 6.1 0.9 - - - -
615A LEU* 3.7 9.9 - - - +
630D ILE 4.6 10.4 + - - -
631D MET 3.2 0.6 - - - +
632D VAL* 1.3 76.9 - - - +
634D VAL* 1.3 59.6 + - - +
636D ALA* 3.1 10.2 + - - +
637D PHE* 2.9 23.6 + - - +
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Residues in contact with VAL 634 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
820A VAL* 5.4 9.3 - - - +
823A GLY 5.8 2.7 - - - -
824A ILE* 5.8 8.1 - - + +
631D MET* 3.5 14.1 + - + +
632D VAL 3.3 0.4 - - - -
633D SER* 1.3 78.5 - - - +
635D TRP* 1.3 59.0 + - - +
637D PHE* 3.2 9.0 + - - +
638D PHE* 2.9 27.9 + - - +
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Residues in contact with TRP 635 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
820A VAL* 6.1 1.8 - - - -
612D LEU* 5.9 2.9 - - + -
631D MET 3.7 3.4 + - - +
632D VAL* 3.2 19.1 + - + +
633D SER 3.2 0.4 - - - -
634D VAL* 1.3 79.1 - - - +
636D ALA* 1.3 56.9 + - - +
638D PHE* 3.5 7.0 + - - +
639D ALA* 2.9 28.4 + - - +
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Residues in contact with ALA 636 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
615A LEU* 3.6 22.1 - - + +
616A ASN 4.9 4.9 - - - +
612D LEU* 4.5 18.0 - - + +
632D VAL 2.9 13.2 + - - +
633D SER* 3.1 12.5 + - - +
635D TRP* 1.3 74.4 - - - +
637D PHE* 1.3 61.3 + - - +
639D ALA* 3.4 7.7 + - - +
640D VAL* 2.9 26.9 + - - +
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Residues in contact with PHE 637 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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615A LEU* 3.9 14.6 - - + +
633D SER 2.9 12.6 + - - +
634D VAL* 3.2 12.5 + - - +
636D ALA* 1.3 76.0 - - - +
638D PHE* 1.3 59.1 + - - +
640D VAL* 3.1 8.2 + - - +
641D ILE* 2.9 27.6 + - - +
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Residues in contact with PHE 638 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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816A VAL* 5.3 3.6 - - + +
820A VAL* 3.9 26.9 - - + -
634D VAL 2.9 15.9 + - - +
635D TRP* 3.8 7.4 - - - +
637D PHE* 1.3 76.2 - - - +
639D ALA* 1.3 57.0 + - - +
641D ILE* 3.4 7.2 + - - +
642D PHE* 2.9 28.6 + - - +
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Residues in contact with ALA 639 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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612D LEU 3.3 27.6 - - - +
613D VAL* 3.6 22.8 - - + +
635D TRP 2.9 18.4 + - - +
636D ALA 3.6 4.5 - - - +
638D PHE* 1.3 75.8 - - - +
640D VAL* 1.3 59.1 + - - +
642D PHE* 3.7 7.0 - - - +
643D LEU* 2.9 29.3 + - - +
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Residues in contact with VAL 640 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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614A LEU 5.6 1.6 - - - +
615A LEU* 5.0 11.7 - - - +
616A ASN* 5.6 4.7 - - + -
636D ALA 2.9 15.2 + - - +
637D PHE* 3.1 12.1 + - - +
639D ALA* 1.3 75.2 - - - +
641D ILE* 1.3 58.6 + - - +
643D LEU* 3.4 5.8 + - - +
644D ALA* 2.9 28.6 + - - +
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Residues in contact with ILE 641 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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816A VAL* 6.0 6.7 - - + -
637D PHE 2.9 12.5 + - - +
638D PHE* 3.7 11.0 - - - +
640D VAL* 1.3 75.0 - - - +
642D PHE* 1.3 59.4 + - - +
644D ALA* 3.3 7.6 + - - +
645D SER* 2.9 29.5 + - - -
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Residues in contact with PHE 642 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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613D VAL 5.9 0.7 - - - +
638D PHE 2.9 17.3 + - - +
639D ALA* 3.7 9.2 - - - +
640D VAL 3.3 0.2 - - - -
641D ILE* 1.3 77.3 - - - +
643D LEU* 1.3 58.0 + - - +
645D SER* 3.5 6.5 + - - -
646D TYR* 2.9 28.1 + - - +
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Residues in contact with LEU 643 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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613D VAL 4.8 8.5 + - - +
614D PHE* 5.8 4.0 - - - +
639D ALA 2.9 18.0 + - - +
640D VAL* 3.6 8.1 - - - +
641D ILE 3.2 0.2 - - - -
642D PHE* 1.3 75.6 - - - +
644D ALA* 1.3 60.2 + - - +
646D TYR* 3.1 8.8 + - - +
647D THR* 2.9 30.0 + - - -
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Residues in contact with ALA 644 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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644A VAL 5.6 0.9 - - - +
647A TYR* 5.4 5.4 - - + -
648A THR* 4.6 25.5 - - - +
651A LEU* 4.7 5.9 - - + +
640D VAL 2.9 17.5 + - - +
641D ILE* 3.3 8.9 + - - +
643D LEU* 1.3 75.7 - - - +
645D SER* 1.3 57.8 + - - +
647D THR* 3.4 5.7 + - - -
648D ALA* 2.9 30.5 + - - +
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Residues in contact with SER 645 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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651A LEU* 5.6 2.0 - - - -
641D ILE 2.9 17.0 + - - -
642D PHE* 3.8 7.9 - - - -
644D ALA* 1.3 72.1 - - - +
646D TYR* 1.3 57.1 + - - +
647D THR 3.1 5.4 - - - -
648D ALA* 4.4 5.4 - - - +
649D ASN* 2.9 37.1 + - - +
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Residues in contact with TYR 646 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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645C ALA* 4.2 13.1 - - + +
553D PRO* 5.7 2.0 - - - +
642D PHE 2.9 18.4 + - - +
643D LEU* 3.1 10.3 + - - +
645D SER* 1.3 75.8 - - - +
647D THR* 1.3 56.6 + - - +
649D ASN* 5.2 1.8 - - - -
650D LEU* 3.2 21.3 + - - +
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Residues in contact with THR 647 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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648A THR* 5.5 7.0 - - - -
647B THR* 6.1 3.6 - - - -
645C ALA* 4.9 12.1 - - - -
648C THR* 5.3 12.8 - - - -
649C ALA* 4.6 3.3 - - - +
643D LEU 2.9 14.3 + - - -
644D ALA* 3.8 6.1 - - - -
645D SER 3.1 0.2 - - - -
646D TYR* 1.3 78.9 - - - +
648D ALA* 1.3 61.0 + - - +
649D ASN 3.4 0.2 - - - -
650D LEU* 3.4 4.8 + - - +
651D ALA* 2.9 29.2 + - - +
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Residues in contact with ALA 648 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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648A THR* 4.0 4.0 - - - +
651A LEU* 3.6 17.5 - - + +
652A ALA* 3.6 40.1 - - + +
655A LEU* 5.5 1.3 - - + -
644D ALA 2.9 18.6 + - - +
645D SER* 4.1 3.8 - - - +
647D THR* 1.3 77.1 - - - +
649D ASN* 1.3 56.9 + - - +
651D ALA* 3.1 6.6 + - - +
652D ALA* 2.9 27.2 + - - +
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Residues in contact with ASN 649 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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655A LEU* 5.6 3.3 - - - +
553D PRO* 3.5 24.7 - - + +
645D SER* 2.9 19.8 + - - +
646D TYR* 5.2 1.1 - - - -
648D ALA* 1.3 78.0 - - - +
650D LEU* 1.3 56.0 + - - +
652D ALA* 3.3 9.1 + - - +
653D PHE* 2.9 30.0 + - - +
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Residues in contact with LEU 650 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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645C ALA* 4.6 7.4 - - + +
646C SER* 5.9 0.7 - - - -
649C ALA* 3.7 15.7 - - + +
553D PRO* 3.7 18.2 - - + +
646D TYR 3.2 23.8 + - - +
647D THR* 3.4 7.5 + - - +
648D ALA 3.2 0.4 - - - -
649D ASN* 1.3 77.2 - - - +
651D ALA* 1.3 58.8 + - - +
653D PHE* 3.4 2.3 + - - +
654D MET* 3.1 29.6 + - - +
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Residues in contact with ALA 651 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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652A ALA* 4.5 12.3 - - + -
656A VAL* 5.3 1.0 - - - +
651B ALA* 6.4 0.2 - - + -
649C ALA* 3.9 13.1 - - - +
652C ALA* 4.4 21.8 - - + -
653C ALA* 5.4 1.0 - - - +
647D THR 2.9 14.1 + - - +
648D ALA* 3.1 11.6 + - - +
650D LEU* 1.3 76.2 - - - +
652D ALA* 1.3 62.0 + - - +
654D MET* 3.4 3.3 + - - +
655D ILE* 3.3 26.9 + - - +
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Residues in contact with ALA 652 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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652A ALA 5.3 1.1 + - - +
655A LEU* 4.3 18.6 - - + +
656A VAL* 4.2 26.3 - - + +
648D ALA 2.9 14.6 + - - +
649D ASN* 3.3 10.7 + - - +
651D ALA* 1.3 77.4 - - - +
653D PHE* 1.3 58.8 + - - +
655D ILE* 3.8 2.9 + - - -
656D GLN* 3.4 25.6 + - - +
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Residues in contact with PHE 653 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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552D GLU* 5.7 2.9 - - + -
553D PRO* 3.8 22.0 - - + -
649D ASN 2.9 17.3 + - - +
650D LEU* 4.0 3.6 - - - +
651D ALA 3.3 0.2 - - - -
652D ALA* 1.3 76.2 - - - +
654D MET* 1.3 58.7 + - - +
655D ILE 3.4 1.3 - - - -
656D GLN* 4.6 3.1 - - - +
657D GLU* 3.8 22.7 - - - +
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Residues in contact with MET 654 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
649C ALA* 4.3 22.4 - - + +
650C ASN* 5.2 2.0 - - - +
653C ALA* 3.3 17.8 - - + +
650D LEU 3.1 17.6 + - - +
651D ALA 3.4 3.1 + - - +
652D ALA 3.3 0.2 - - - -
653D PHE* 1.3 78.4 - - - +
655D ILE* 1.3 59.2 + - - +
656D GLN 3.7 1.6 - - - -
657D GLU* 5.2 2.5 - - - -
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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) + - + + + + + -
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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