Contacts of the helix formed by residues 642 - 659 (chain A) in PDB entry 4OSI
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 GLY 642 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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607A GLY 4.4 3.2 + - - -
641A ASP* 1.3 74.8 - - - +
643A GLY* 1.3 65.4 + - - +
644A LYS 3.1 3.1 - - - -
645A GLN* 2.9 6.2 + - - +
646A ALA* 2.8 26.3 + - - +
13I T 4.1 29.7 + - - +
14I C 3.6 20.2 + - - -
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Residues in contact with GLY 643 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
612A ALA* 4.2 7.9 - - - +
637A ILE 3.8 10.6 - - - +
638A ALA* 3.5 20.4 - - - -
640A HIS* 2.8 19.2 + - - -
642A GLY* 1.3 76.1 - - - +
644A LYS* 1.3 57.2 + - - +
646A ALA* 3.2 3.6 + - - +
647A LEU* 2.9 32.5 + - - +
13I T 4.9 1.0 + - - -
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Residues in contact with LYS 644 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
611A GLN* 3.0 49.2 + - + +
612A ALA* 4.1 5.9 - - - +
615A THR* 3.2 36.3 - - - +
618A ARG* 5.7 3.1 - - - +
642A GLY 3.1 0.6 - - - -
643A GLY* 1.3 71.6 - - - +
645A GLN* 1.3 79.3 + - - +
647A LEU* 3.2 1.9 + - - +
648A GLU* 3.0 47.1 + - - +
13I T 4.1 10.9 + - - +
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Residues in contact with GLN 645 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
642A GLY* 2.9 7.4 + - - +
644A LYS* 1.3 90.0 - - - +
646A ALA* 1.3 55.8 + - - +
648A GLU* 3.8 15.7 + - - +
649A THR* 2.5 39.2 + - - -
678A ARG* 2.8 44.2 + - + +
13I T 3.4 35.7 + - - +
14I C 3.5 33.9 - - - +
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Residues in contact with ALA 646 (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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637A ILE* 3.6 25.8 - - + +
640A HIS* 6.5 0.7 - - + -
642A GLY 2.8 11.7 + - - +
643A GLY* 3.4 9.4 - - - +
645A GLN* 1.3 78.3 - - - +
647A LEU* 1.3 57.5 + - - +
649A THR* 3.6 1.4 - - - -
650A VAL* 2.9 33.4 + - - +
672A ALA* 4.0 14.6 - - + +
674A ASN 5.2 1.6 - - - +
677A GLY* 4.4 11.9 - - - +
678A ARG 4.1 11.4 - - - +
681A LEU* 6.2 0.2 - - - -
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Residues in contact with LEU 647 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
612A ALA 4.5 1.1 - - - +
615A THR* 3.8 27.1 - - + +
616A VAL* 3.5 34.8 - - + +
619A LEU* 4.0 8.8 - - + +
623A LEU* 3.8 27.1 - - + +
634A VAL* 4.0 14.4 - - + +
637A ILE* 4.0 28.5 - - + -
638A ALA* 3.6 13.2 - - + +
643A GLY 2.9 18.6 + - - +
644A LYS 3.2 0.4 + - - -
646A ALA* 1.3 76.3 - - - +
648A GLU* 1.3 57.0 + - - +
650A VAL* 3.6 3.4 + - + +
651A GLN* 3.0 27.0 + - - +
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Residues in contact with GLU 648 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
615A THR* 4.6 4.9 - - + -
618A ARG* 4.0 24.5 + - - +
619A LEU* 4.5 3.4 - - + -
644A LYS* 3.0 50.8 + - - +
645A GLN* 3.8 17.2 + - - +
647A LEU* 1.3 73.7 - - - +
649A THR* 1.3 68.0 + - - +
651A GLN* 3.1 10.0 + - - +
652A ARG* 2.9 36.5 + - + +
678A ARG* 5.6 0.6 + - - -
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Residues in contact with THR 649 (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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645A GLN 2.5 22.8 + - - -
646A ALA* 3.6 3.8 - - - -
648A GLU* 1.3 77.6 - - - +
650A VAL* 1.3 57.5 + - - +
652A ARG* 3.3 13.4 + - - +
653A LEU* 2.9 52.5 + - + +
678A ARG* 2.8 54.1 - - - +
681A LEU* 3.8 9.6 - - + -
682A GLU* 4.2 1.8 - - + -
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Residues in contact with VAL 650 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
623A LEU* 5.1 7.2 - - + -
629A LEU* 4.7 13.7 - - + -
637A ILE* 4.6 13.2 - - + -
646A ALA 2.9 16.9 + - - +
647A LEU* 3.9 6.1 - - - +
649A THR* 1.3 74.1 - - - +
651A GLN* 1.3 68.2 + - - +
652A ARG 2.9 0.2 + - - -
653A LEU 4.5 0.2 - - - +
654A LEU* 2.9 46.3 + - + +
668A VAL* 4.1 13.2 - - + -
669A VAL* 5.7 1.3 - - + +
672A ALA* 3.5 25.1 - - + -
681A LEU* 3.4 24.5 - - + -
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Residues in contact with GLN 651 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
618A ARG* 5.5 0.3 + - - -
619A LEU* 3.4 31.5 - - + +
622A VAL* 4.5 18.3 - - - +
623A LEU* 4.2 19.8 - - + +
627A HIS* 3.6 21.9 + - - +
647A LEU 3.0 15.9 + - - +
648A GLU* 3.1 12.3 + - + +
650A VAL* 1.3 80.0 - - - +
652A ARG* 1.3 69.6 + - + +
654A LEU* 5.3 0.2 - - - -
655A PRO* 4.1 5.7 - - - +
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Residues in contact with ARG 652 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
648A GLU* 2.9 24.7 + - + +
649A THR* 3.8 25.6 + - - +
651A GLN* 1.3 87.5 - - + +
653A LEU* 1.3 80.7 + - + +
654A LEU 3.6 0.2 - - - -
655A PRO* 3.9 9.9 - - - +
656A VAL* 4.5 4.7 - - - +
678A ARG* 4.1 10.1 - - - +
682A GLU* 3.8 21.4 + - - +
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Residues in contact with LEU 653 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
649A THR* 2.9 39.0 + - + +
652A ARG* 1.3 95.9 - - - +
654A LEU* 1.3 68.6 + - - +
655A PRO* 3.3 3.1 - - - -
656A VAL* 3.4 18.7 - - + +
657A LEU* 3.2 25.5 + - + +
668A VAL* 6.0 0.9 - - - -
681A LEU* 4.2 8.5 - - + -
682A GLU* 4.1 20.0 - - + +
685A VAL* 3.7 35.2 - - + -
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Residues in contact with LEU 654 (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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623A LEU* 6.0 0.9 - - + -
627A HIS* 3.2 50.9 - - + +
629A LEU* 4.4 21.1 - - + -
650A VAL* 2.9 32.5 + - + +
651A GLN* 5.3 0.2 - - - -
653A LEU* 1.3 76.3 - - - +
655A PRO* 1.4 64.9 - - + +
657A LEU* 3.7 3.1 - - - +
658A CYS* 2.9 52.2 + - + +
659A GLN* 5.8 1.6 - - - +
665A PRO* 5.1 9.0 - - + -
668A VAL* 4.9 16.1 - - + +
669A VAL* 6.1 1.1 - - + -
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Residues in contact with PRO 655 (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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627A HIS* 3.7 24.2 - - + +
651A GLN 4.1 4.3 - - - +
652A ARG 3.9 12.3 - - - +
653A LEU 3.5 2.7 - - - -
654A LEU* 1.4 99.3 - - + +
656A VAL* 1.3 57.6 + - + +
658A CYS* 4.9 0.2 - - + -
659A GLN* 2.5 55.4 + - + +
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Residues in contact with VAL 656 (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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652A ARG 4.5 3.4 - - - +
653A LEU* 3.4 39.3 - - + +
655A PRO* 1.3 76.9 - - + +
657A LEU* 1.3 56.5 + - - +
659A GLN* 4.8 0.4 - - - -
660A ALA* 2.9 40.3 - - + +
661A HIS* 3.1 26.0 + - + +
685A VAL* 4.5 15.0 - - + -
689A SER* 5.4 2.9 - - - +
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Residues in contact with LEU 657 (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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653A LEU* 3.2 18.9 + - + +
654A LEU 3.7 2.0 - - - +
655A PRO 3.2 0.4 - - - -
656A VAL* 1.3 79.8 - - - +
658A CYS* 1.3 62.7 + - - +
661A HIS* 3.6 8.9 - - - +
662A GLY 3.2 7.8 + - - -
663A LEU* 3.0 44.3 + - + +
668A VAL* 4.1 19.5 - - + -
671A ILE* 6.0 0.9 - - + -
681A LEU* 4.6 15.7 - - + -
684A ILE* 4.3 7.4 - - + -
685A VAL* 3.5 49.4 - - + -
688A LEU* 4.1 22.0 - - + -
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Residues in contact with CYS 658 (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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654A LEU* 2.9 35.0 + - + +
655A PRO* 4.0 1.6 - - + +
657A LEU* 1.3 73.8 - - - +
659A GLN* 1.3 75.7 + - + +
662A GLY* 2.9 19.1 - - - -
663A LEU 3.1 22.7 + - - +
664A THR 4.2 1.6 - - - -
665A PRO* 3.7 35.9 - - - -
668A VAL* 4.6 6.7 - - - -
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Residues in contact with GLN 659 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
654A LEU* 5.8 1.7 - - - +
655A PRO* 2.5 44.1 + - + +
656A VAL* 3.9 0.7 - - - -
658A CYS* 1.3 74.4 - - - +
660A ALA* 1.3 55.1 + - - +
661A HIS 2.5 19.9 + - - -
662A GLY* 2.5 16.6 + - - -
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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
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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