Contacts of the helix formed by residues 637 - 648 (chain S) in PDB entry 1BKD
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 PRO 637 (chain S).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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631S TYR* 3.2 31.8 - - + +
632S ARG* 4.4 10.5 - - + +
635S CYS 4.2 3.4 - - - +
636S LYS* 1.3 85.1 - - + +
638S GLN* 1.3 63.3 + - + +
640S LEU* 3.2 4.3 + - - +
641S LEU 3.1 18.5 + - - -
696S TRP* 3.5 7.6 - - + -
703S ASP* 4.0 17.7 - - + +
707S ASP* 6.0 1.6 - - + +
710S LEU* 3.8 22.5 - - + +
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Residues in contact with GLN 638 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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636S LYS* 3.2 4.1 - - + +
637S PRO* 1.3 80.6 - - + +
639S GLU* 1.3 65.1 + - + +
641S LEU 3.5 0.5 + - - -
642S SER* 3.3 11.0 + - - -
707S ASP* 2.9 28.9 + - - +
709S TYR* 3.8 18.2 - - - -
710S LEU* 3.4 32.5 - - + +
713S ARG* 2.9 53.3 + - - +
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Residues in contact with GLU 639 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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634S PHE 5.1 0.3 - - - +
635S CYS* 3.8 15.1 - - - -
636S LYS* 2.8 52.4 + - + +
638S GLN* 1.3 75.3 - - + +
640S LEU* 1.3 60.3 + - - +
642S SER* 3.4 7.9 + - - -
643S LEU* 2.9 37.8 + - + +
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Residues in contact with LEU 640 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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610S ILE* 3.8 23.8 - - + -
613S LEU* 5.5 1.8 - - + -
627S PHE* 4.0 15.0 - - + -
628S LEU* 4.2 14.6 - - + -
631S TYR* 3.9 29.4 - - + -
635S CYS* 3.7 8.9 - - - -
636S LYS 3.0 9.8 + - - +
637S PRO 3.3 8.5 - - - +
639S GLU* 1.3 75.5 - - - +
641S LEU* 1.3 60.3 + - - +
643S LEU* 3.2 3.4 + - - +
644S ILE* 2.9 41.7 + - + +
692S VAL* 5.7 0.2 - - + -
696S TRP* 3.4 36.1 - - + -
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Residues in contact with LEU 641 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
637S PRO 3.1 8.4 + - - +
638S GLN 3.9 7.2 - - - +
639S GLU 3.4 0.2 - - - -
640S LEU* 1.3 79.0 - - - +
642S SER* 1.3 58.6 + - - +
644S ILE* 3.3 11.2 + - + +
645S ILE* 2.9 47.1 + - + +
693S CYS* 5.4 0.7 - - - -
696S TRP* 3.8 19.0 - - + -
710S LEU* 3.7 24.5 - - + +
713S ARG* 3.5 42.4 - - + +
714S MET* 3.8 33.0 - - + +
717S PHE* 4.9 4.0 - - + -
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Residues in contact with SER 642 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
638S GLN 3.3 6.1 + - - -
639S GLU* 3.6 10.7 - - - -
641S LEU* 1.3 79.8 - - - +
643S LEU* 1.3 58.2 + - - +
645S ILE* 3.4 4.4 + - - +
646S GLU* 2.9 30.0 + - - +
713S ARG* 2.9 32.9 + - - +
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Residues in contact with LEU 643 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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577S PHE* 3.6 9.3 - - + -
606S VAL* 3.6 26.2 - - + -
607S ILE* 3.9 27.6 - - + -
610S ILE* 3.4 37.4 - - + +
635S CYS* 4.3 5.6 - - - -
639S GLU* 2.9 28.5 + - + +
640S LEU 3.2 1.3 + - - +
642S SER* 1.3 74.1 - - - +
644S ILE* 1.3 60.9 + - - +
646S GLU* 3.3 15.7 + - - +
647S ARG* 2.9 28.8 + - - +
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Residues in contact with ILE 644 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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610S ILE* 5.1 7.9 - - + -
613S LEU* 5.7 2.5 - - + -
614S THR* 5.7 3.1 - - - +
640S LEU* 2.9 34.4 + - + +
641S LEU* 3.5 11.0 - - + +
643S LEU* 1.3 73.5 - - - +
645S ILE* 1.3 63.7 + - - +
647S ARG* 3.1 8.9 + - - +
648S PHE* 3.0 26.2 + - - +
689S VAL* 3.5 27.2 - - + +
692S VAL* 3.4 34.3 - - + -
693S CYS* 4.1 15.5 - - - -
696S TRP* 4.2 18.4 - - + -
717S PHE* 4.5 5.4 - - + -
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Residues in contact with ILE 645 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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641S LEU* 2.9 32.4 + - + +
642S SER* 3.7 5.6 - - - +
644S ILE* 1.3 77.7 - - + +
646S GLU* 1.3 62.6 + - - +
648S PHE* 3.2 1.7 + - - +
649S GLU* 3.2 47.4 + - - +
713S ARG* 3.8 24.5 - - - +
717S PHE* 3.7 49.6 - - + -
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Residues in contact with GLU 646 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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575S TYR 5.9 0.5 - - - -
576S ARG* 2.7 34.9 + - - +
577S PHE* 3.6 20.3 - - + -
607S ILE* 5.1 6.9 - - - +
642S SER 2.9 18.1 + - - +
643S LEU* 3.6 20.7 - - - +
644S ILE 3.3 0.2 - - - -
645S ILE* 1.3 76.6 - - - +
647S ARG* 1.3 50.9 + - - +
649S GLU* 4.0 12.4 - - - +
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Residues in contact with ARG 647 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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576S ARG* 2.7 43.1 + - - +
577S PHE* 3.6 28.7 - - + +
610S ILE* 3.5 6.7 + - + -
611S GLU* 3.0 47.9 + - - +
614S THR* 3.1 28.9 + - + +
615S TYR* 4.8 0.2 - - - +
616S HIS* 4.8 4.9 + - - +
643S LEU 2.9 13.1 + - - +
644S ILE* 3.4 12.3 - - - +
645S ILE 3.1 0.4 - - - -
646S GLU* 1.3 74.0 - - - +
648S PHE* 1.3 58.1 + - - +
650S ILE* 3.3 11.1 - - - +
681S TYR* 3.8 14.6 + - - -
685S VAL* 3.5 24.8 - - + +
689S VAL* 3.9 17.7 - - + -
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Residues in contact with PHE 648 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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644S ILE 3.0 12.2 + - - +
645S ILE 3.2 7.8 + - - +
647S ARG* 1.3 77.4 - - - +
649S GLU* 1.3 61.0 + - + +
650S ILE* 2.8 23.9 + - - +
686S GLN* 3.3 64.4 + - + +
689S VAL* 3.9 18.8 - - + +
690S LEU* 3.7 26.2 - - + -
717S PHE* 3.8 27.8 - + + -
720S THR* 5.4 4.9 - - + -
721S VAL* 4.6 19.3 - - + -
722S ARG* 4.7 17.5 - - - -
726S MET* 4.5 7.0 - - + -
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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
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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