Contacts of the helix formed by residues 681 - 692 (chain A) in PDB entry 2ADS
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 TYR 681 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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673A ILE* 6.1 0.2 - - - +
675A LEU* 4.6 15.0 - - + +
679A VAL 3.0 4.2 + - - -
680A HIS* 1.3 110.7 + + - +
682A SER* 1.3 63.6 + - - +
683A ASP* 3.0 4.6 - - - +
684A LYS* 2.9 58.8 + - + +
685A ILE* 3.1 16.9 + - + +
705A TRP 3.8 13.2 - - - +
706A LEU 3.3 21.8 - - - -
3G C 3.1 28.5 + - - -
4G C 3.5 26.3 + - - -
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Residues in contact with SER 682 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
500A GLY 6.1 0.2 - - - -
502A ASP* 3.8 14.1 - - - -
518A PHE* 3.6 27.6 - - - -
520A LYS* 2.8 36.4 + - - -
571A ASP* 6.3 0.2 - - - -
678A THR 3.6 7.3 + - - -
679A VAL* 3.8 9.8 - - - -
680A HIS 2.9 3.0 + - - -
681A TYR* 1.3 75.5 - - - +
683A ASP* 1.3 62.3 + - - +
685A ILE* 3.1 13.8 + - - +
686A THR* 3.1 18.9 + - - +
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Residues in contact with ASP 683 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
901 CA 3.1 16.5 - - - -
502A ASP* 3.3 13.9 + - - +
504A SER* 4.1 0.7 + - - -
571A ASP* 2.8 34.5 - - - +
600A LYS* 2.8 19.7 + - - -
675A LEU* 6.4 0.2 - - + -
679A VAL 3.9 4.2 + - - +
681A TYR* 4.7 2.0 - - - +
682A SER* 1.3 79.0 - - - +
684A LYS* 1.3 56.2 + - + +
686A THR* 2.9 16.3 + - - -
687A LYS 4.3 0.3 + - - -
12M G 2.5 23.3 + - - +
13M G 2.7 36.3 + - - +
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Residues in contact with LYS 684 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
675A LEU* 6.4 0.4 - - - -
681A TYR* 2.9 60.9 + - + +
683A ASP* 1.3 77.5 - - + +
685A ILE* 1.3 66.7 + - + +
686A THR 3.2 0.4 - - - -
687A LYS* 3.1 19.4 + - - +
688A LEU* 3.2 9.9 + - - +
1G A 5.5 15.8 + - - +
13M G 4.4 8.1 - - - +
14M G 4.3 25.8 + - - +
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Residues in contact with ILE 685 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
447A LEU* 5.4 1.3 - - + -
518A PHE* 3.9 16.4 - - + -
533A LEU* 3.8 28.9 - - + -
681A TYR* 3.1 13.4 + - + +
682A SER 3.1 6.4 + - - +
684A LYS* 1.3 75.1 - - + +
686A THR* 1.3 67.5 + - - +
688A LEU* 3.1 24.4 + - + +
689A MSE 3.2 21.3 + - + +
704A TYR* 4.5 9.6 - - + +
705A TRP* 3.4 44.0 - - + +
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Residues in contact with THR 686 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
502A ASP* 3.2 20.7 + - - +
504A SER* 2.9 25.8 + - - +
516A VAL* 3.5 33.2 - - + +
518A PHE* 3.7 20.6 - - + -
682A SER 3.1 6.8 + - - +
683A ASP 2.9 19.1 + - - -
685A ILE* 1.3 77.5 - - - +
687A LYS* 1.3 62.7 + - - +
689A MSE 3.3 3.3 + - - +
690A LEU* 3.0 27.4 + - - +
13M G 5.3 0.9 - - - -
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Residues in contact with LYS 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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440A ASP* 4.9 6.5 + - - -
506A ILE* 5.9 3.6 - - + -
684A LYS 3.1 9.7 + - - +
686A THR* 1.3 78.6 + - - +
688A LEU* 1.3 80.8 + - + +
690A LEU* 3.0 12.7 + - + +
691A ARG* 2.9 72.3 + - + +
13M G 3.3 34.8 - - - +
14M G 3.6 37.1 + - - +
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Residues in contact with LEU 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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439A TYR* 6.4 0.9 - - + -
440A ASP* 3.2 48.0 - - + +
443A LYS* 4.3 14.8 - - + -
444A ARG* 3.7 38.4 + - + +
447A LEU* 5.9 1.1 - - + -
684A LYS 3.2 4.4 + - - +
685A ILE* 3.1 27.2 + - + +
687A LYS* 1.3 92.5 - - + +
689A MSE 1.3 65.4 + - + +
691A ARG* 4.3 2.4 - - + +
692A GLY 3.3 14.9 + - - -
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Residues in contact with MSE 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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444A ARG* 3.7 36.8 - - + +
447A LEU* 3.9 31.0 - - + -
516A VAL* 4.6 10.3 - - + -
533A LEU* 3.9 23.1 - - + -
535A SER* 6.0 1.3 - - - -
685A ILE* 3.2 17.0 + - + +
686A THR 3.9 5.2 - - - +
687A LYS 3.1 0.4 - - - -
688A LEU* 1.3 83.1 - - + +
690A LEU* 1.3 58.8 + - - +
692A GLY* 2.8 26.5 + - - +
694A GLU 4.4 4.7 - - - +
695A PRO* 5.5 1.9 - - - +
696A ILE* 3.7 42.7 - - + +
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Residues in contact with LEU 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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504A SER* 4.3 22.0 - - - -
505A ARG 4.8 0.4 - - - +
506A ILE* 3.6 35.0 - - + -
514A ASN* 3.1 57.8 - - + +
515A ALA* 3.8 0.7 - - - +
516A VAL* 3.6 13.9 - - + +
686A THR 3.0 28.2 + - - +
687A LYS* 3.5 9.9 - - + +
689A MSE 1.3 77.4 - - - +
691A ARG* 1.3 63.7 + - - +
692A GLY 3.2 6.8 + - - +
693A ILE* 5.1 0.5 - - - -
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Residues in contact with ARG 691 (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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437A LEU* 4.6 20.2 - - - +
440A ASP* 5.8 1.2 + - - -
444A ARG* 4.9 4.0 - - - +
506A ILE* 5.0 2.7 - - - +
687A LYS* 2.9 53.9 + - + +
688A LEU* 4.4 3.4 - - - +
690A LEU* 1.3 72.9 - - - +
692A GLY* 1.3 61.6 + - - +
693A ILE* 3.0 12.8 + - - +
14M G 4.8 13.5 + - - -
15M G 6.0 0.8 - - - -
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Residues in contact with GLY 692 (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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444A ARG* 3.7 24.7 - - - +
688A LEU 3.3 8.4 + - - -
689A MSE 2.8 23.5 + - - +
690A LEU 3.1 8.0 - - - +
691A ARG* 1.3 74.5 - - - +
693A ILE* 1.3 65.7 + - - +
694A GLU 3.3 12.0 + - - +
695A PRO* 5.0 0.7 - - - +
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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