Contacts of the helix formed by residues 676 - 690 (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 676 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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641A ASP 4.6 4.0 + - - -
674A ASN* 4.9 2.2 - - - -
675A GLY* 1.3 72.6 - - - -
677A GLY* 1.3 54.5 + - - +
679A PRO* 3.1 14.2 - - - +
680A ALA* 2.8 39.2 + - - +
711A GLY* 5.2 2.7 - - - -
14I C 4.3 15.1 + - - +
15I T 3.8 21.3 + - - +
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Residues in contact with GLY 677 (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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646A ALA* 4.4 8.2 - - - +
671A ILE 4.5 4.3 - - - -
672A ALA* 3.9 21.5 - - - -
674A ASN 3.3 15.3 + - - -
676A GLY* 1.3 75.1 - - - +
678A ARG* 1.3 66.1 + - - +
680A ALA* 2.9 14.1 + - - +
681A LEU* 2.9 19.2 + - - +
14I C 5.2 1.4 + - - -
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Residues in contact with ARG 678 (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* 2.8 39.8 + - + +
646A ALA* 4.1 9.3 - - - +
648A GLU* 5.6 0.6 + - - -
649A THR* 2.8 36.6 - - - +
652A ARG* 4.1 10.7 - - - +
677A GLY* 1.3 73.0 - - - +
679A PRO* 1.3 73.3 - - + +
681A LEU* 3.3 2.6 + - - +
682A GLU* 2.6 70.2 + - - +
14I C 3.6 15.4 + - - +
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Residues in contact with PRO 679 (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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676A GLY* 3.1 27.4 - - - +
678A ARG* 1.3 95.6 - - + +
680A ALA* 1.3 53.9 + - - +
682A GLU* 3.7 11.5 - - + +
683A SER* 2.9 32.6 + - - -
712A ARG* 3.1 40.0 - - + +
14I C 3.7 23.8 - - - +
15I T 3.8 16.2 - - - +
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Residues in contact with ALA 680 (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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671A ILE* 3.7 22.0 - - + +
676A GLY 2.8 24.7 + - - +
677A GLY* 3.5 3.4 - - - +
679A PRO* 1.3 69.3 - - - +
681A LEU* 1.3 69.7 + - - +
683A SER* 3.4 3.3 + - - -
684A ILE* 3.0 25.3 + - - +
707A ALA* 4.4 5.3 - - + +
711A GLY* 3.6 26.0 - - - -
712A ARG 3.9 10.0 - - - +
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Residues in contact with LEU 681 (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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646A ALA 4.9 0.2 - - - +
649A THR* 3.8 19.1 - - + +
650A VAL* 3.4 42.6 - - + -
653A LEU* 4.2 9.9 - - + -
657A LEU* 4.6 13.0 - - + -
668A VAL* 4.2 19.3 - - + +
671A ILE* 3.4 33.7 - - + -
672A ALA* 4.4 4.3 - - + +
677A GLY 2.9 14.1 + - - +
678A ARG 3.5 7.2 - - - +
680A ALA* 1.3 80.5 - - - +
682A GLU* 1.3 64.0 + - - +
684A ILE* 3.0 3.1 + - + +
685A VAL* 2.9 28.7 + - + +
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Residues in contact with GLU 682 (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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649A THR* 4.2 2.0 - - + -
652A ARG* 3.8 9.9 + - - +
653A LEU* 4.1 20.0 - - + -
678A ARG* 2.6 70.0 + - - +
679A PRO* 3.7 10.8 - - + +
681A LEU* 1.3 72.7 - - - +
683A SER* 1.3 55.7 + - - +
685A VAL* 3.9 2.7 - - - +
686A ALA* 2.9 30.8 + - - +
712A ARG* 5.1 3.3 + - - -
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Residues in contact with SER 683 (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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679A PRO 2.9 21.4 + - - -
680A ALA 3.8 2.5 + - - -
682A GLU* 1.3 69.9 - - - +
684A ILE* 1.3 59.6 + - - +
686A ALA* 3.7 5.8 - - - +
687A GLN* 3.0 28.6 + - - +
712A ARG* 3.9 27.5 - - - +
715A LEU* 3.2 31.6 - - - +
716A ASP* 4.6 3.6 + - - -
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Residues in contact with ILE 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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657A LEU* 4.3 14.6 - - + -
663A LEU* 4.7 6.5 - - + -
671A ILE* 4.6 6.7 - - + -
680A ALA 3.0 13.7 + - - +
681A LEU* 3.0 9.8 + - + +
683A SER* 1.3 74.1 + - - +
685A VAL* 1.3 68.0 + - - +
687A GLN* 3.0 4.7 + - - +
688A LEU* 2.9 42.1 + - + +
703A LEU* 3.4 42.4 - - + -
704A VAL* 4.1 6.5 - - + +
707A ALA* 3.8 13.7 - - + -
715A LEU* 3.2 24.9 - - + -
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Residues in contact with VAL 685 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
653A LEU* 3.7 36.1 - - + -
656A VAL* 4.5 17.9 - - + -
657A LEU* 3.5 42.4 - - + -
661A HIS* 4.7 1.3 + - + -
681A LEU 2.9 19.2 + - - +
682A GLU* 3.9 4.0 - - - +
684A ILE* 1.3 71.1 - - - +
686A ALA* 1.3 64.1 + - - +
688A LEU* 3.2 2.6 + - - +
689A SER* 2.9 27.9 + - - -
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Residues in contact with ALA 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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682A GLU 2.9 18.6 + - - +
683A SER* 3.7 7.0 - - - +
685A VAL* 1.3 76.2 - - - +
687A GLN* 1.3 54.5 + - - +
688A LEU 2.7 12.0 + - - -
689A SER* 3.0 13.0 + - - -
690A ARG* 3.1 19.5 + - + +
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Residues in contact with GLN 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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683A SER 3.0 18.8 + - - +
684A ILE* 3.0 9.5 + - - +
686A ALA* 1.3 75.0 - - - +
688A LEU* 1.3 57.1 + - - +
690A ARG 4.9 1.7 - - - +
691A PRO* 3.0 20.2 - - - +
692A ASP* 3.6 19.2 + - - +
695A LEU* 3.0 56.5 + - + +
696A ALA 5.1 0.2 - - - +
703A LEU* 3.5 28.1 - - + +
715A LEU* 4.9 7.4 - - + -
719A LYS* 5.3 1.7 - - - +
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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
----------------------------------------------------------
657A LEU* 4.1 8.3 - - + -
661A HIS* 2.8 51.8 + - + +
663A LEU* 4.2 15.5 - - + -
684A ILE* 2.9 34.2 + - + +
685A VAL* 3.8 3.6 - - - +
686A ALA 2.7 4.6 + - - -
687A GLN* 1.3 80.2 - - - +
689A SER* 1.3 58.7 + - - +
690A ARG 3.5 0.4 - - - -
691A PRO* 3.0 18.8 - - + +
700A ASN* 3.9 20.2 - - + +
703A LEU* 3.6 30.5 - - + -
704A VAL* 6.4 0.2 - - + -
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Residues in contact with SER 689 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
656A VAL* 5.4 2.8 - - - +
661A HIS* 3.3 18.7 - - - -
685A VAL* 2.9 20.0 + - - -
686A ALA* 4.2 2.2 - - - -
688A LEU* 1.3 73.1 - - - +
690A ARG* 1.3 69.2 + - - +
691A PRO* 3.2 11.4 - - - +
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Residues in contact with ARG 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 ALA* 3.1 16.3 + - + +
687A GLN* 4.4 1.7 - - - +
689A SER* 1.3 84.4 - - - +
691A PRO* 1.3 65.4 - - - +
692A ASP* 3.2 12.6 + - - +
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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
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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