Contacts of the helix formed by residues 683 - 691 (chain A) in PDB entry 4EG8
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 683 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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679A VAL 2.8 11.9 + - - -
680A THR 3.5 6.7 + - - +
681A ASP 3.3 1.2 - - - -
682A MET* 1.3 80.2 - - - +
684A PRO* 1.3 64.0 - - - +
685A TRP* 3.2 31.9 - - + +
686A LYS* 2.9 40.6 + - + +
687A LEU 3.4 2.9 + - - -
434B ARG* 4.2 15.7 - - - +
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Residues in contact with PRO 684 (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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616A ARG* 6.3 1.1 - - + -
622A ILE* 4.0 16.6 - - + -
679A VAL* 3.1 33.9 - - + +
682A MET* 3.7 4.3 - - + -
683A ALA* 1.3 86.9 - - - +
685A TRP* 1.3 75.3 + - + +
686A LYS 3.2 0.2 - - - -
687A LEU* 3.1 18.0 + - + -
688A VAL* 3.3 13.5 + - - +
695A LEU* 3.5 30.1 - - + +
698A VAL* 4.3 14.8 - - + -
699A LEU* 5.8 1.3 - - + -
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Residues in contact with TRP 685 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
616A ARG* 4.1 37.5 - - + -
621A LYS* 4.2 31.8 - - + +
622A ILE* 4.3 16.0 - - + +
679A VAL* 4.0 16.6 - - + -
680A THR* 4.2 14.6 - - + -
683A ALA* 3.9 16.6 - - + +
684A PRO* 1.3 96.6 - - + +
686A LYS* 1.3 92.8 + - + +
688A VAL* 3.8 17.6 + - - +
689A LYS* 4.7 2.3 + - - +
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Residues in contact with LYS 686 (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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683A ALA* 2.9 22.3 + - + +
685A TRP* 1.3 99.4 - - + +
687A LEU* 1.3 63.8 + - + +
688A VAL 3.4 0.3 + - - -
689A LYS* 3.5 6.4 + - - +
690A THR* 2.9 25.8 + - - -
814A GOL 3.3 43.0 + - - +
434B ARG* 4.2 18.2 - - - +
438B ARG* 4.9 5.3 - - - +
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Residues in contact with LEU 687 (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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682A MET* 3.5 27.1 - - + +
683A ALA 3.8 1.8 - - - +
684A PRO* 3.1 16.2 + - + +
686A LYS* 1.3 75.6 - - + +
688A VAL* 1.3 64.5 + - - +
689A LYS 3.1 2.5 - - - -
690A THR* 4.3 6.3 - - + -
691A ASP* 2.9 51.8 + - + +
692A PRO* 3.4 0.7 - - - +
694A ARG* 3.9 24.7 - - + -
695A LEU* 3.8 19.1 - - + +
698A VAL* 4.1 18.6 - - + -
814A GOL 5.4 0.4 - - - +
430B GLU* 5.1 7.6 - - - +
433B ARG* 5.9 1.3 - - - +
434B ARG* 5.2 11.0 - - - -
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Residues in contact with VAL 688 (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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621A LYS* 3.4 23.8 - - + +
622A ILE* 3.6 9.0 - - - +
624A VAL* 4.3 16.8 - - + -
684A PRO 3.3 10.0 + - - +
685A TRP* 3.8 12.3 - - - +
686A LYS 3.3 0.2 - - - -
687A LEU* 1.3 76.7 - - - +
689A LYS* 1.3 70.3 - - + +
692A PRO* 3.9 15.8 - - - +
695A LEU* 3.3 29.1 - - + +
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Residues in contact with LYS 689 (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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685A TRP 5.6 2.0 - - - +
686A LYS 3.5 6.9 + - - +
687A LEU 3.1 0.2 - - - -
688A VAL* 1.3 90.0 - - + +
690A THR* 1.3 64.9 + - - +
691A ASP 3.7 0.4 - - - -
692A PRO* 4.4 5.9 - - - +
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Residues in contact with THR 690 (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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686A LYS* 2.9 17.6 + - - +
687A LEU* 3.2 8.2 + - + -
689A LYS* 1.3 80.7 - - - +
691A ASP* 1.3 65.8 + - + +
692A PRO* 3.9 3.1 - - - +
814A GOL 3.0 44.9 + - - +
421B HIS* 4.3 14.2 - - + -
437B ILE* 5.3 2.5 - - + -
441B GLU* 4.7 12.7 - - - +
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Residues in contact with ASP 691 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
687A LEU* 2.9 27.9 + - + +
690A THR* 1.3 77.3 - - + +
692A PRO* 1.3 69.7 - - - +
693A GLU* 3.6 11.1 + - - +
694A ARG* 3.1 34.1 + - + +
695A LEU* 3.0 17.8 + - - +
421B HIS* 2.9 37.1 + - + +
424B PRO* 5.7 0.5 - - - +
433B ARG* 4.1 11.3 + - - -
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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