Contacts of the helix formed by residues 692 - 702 (chain A) in PDB entry 5E2Q
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 SER 692 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14A VAL* 3.4 17.0 - - - +
690A GLU* 2.9 37.5 + - - -
691A ALA* 1.3 76.7 - - - +
693A ALA* 1.3 60.2 + - - +
694A ALA* 3.7 4.6 + - - +
695A GLY 3.2 12.1 + - - -
696A LEU* 2.9 28.6 + - - +
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Residues in contact with ALA 693 (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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12A ILE* 6.2 0.7 - - + -
14A VAL* 4.2 10.0 - - + +
90A GLN* 5.1 4.7 - - - +
93A LEU* 3.7 33.2 - - + +
94A VAL* 4.1 15.0 - - + +
97A ALA* 3.9 14.1 - - + +
671A LEU* 6.0 0.7 - - + -
692A SER* 1.3 75.0 - - - +
694A ALA* 1.3 57.8 + - - +
696A LEU* 3.2 3.7 + - - +
697A ILE* 2.9 34.0 + - - +
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Residues in contact with ALA 694 (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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72A PRO* 3.7 31.2 - - + +
73A ASP* 5.8 0.2 - - - +
76A ARG* 6.2 1.1 - - - +
93A LEU* 4.7 11.5 - - + +
690A GLU* 4.8 4.3 - - - +
692A SER* 3.3 7.2 + - - +
693A ALA* 1.3 78.1 - - - +
695A GLY* 1.3 57.3 + - - +
697A ILE* 3.5 5.9 + - - +
698A ARG* 3.0 45.3 + - - +
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Residues in contact with GLY 695 (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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673A VAL* 4.3 0.4 - - - -
689A TYR* 3.6 15.4 - - - +
690A GLU* 3.4 35.8 + - - -
692A SER* 3.2 11.5 + - - -
693A ALA 3.2 0.8 - - - -
694A ALA* 1.3 76.4 - - - +
696A LEU* 1.3 63.4 - - - +
698A ARG* 3.4 8.7 + - - +
699A SER* 3.1 17.2 + - - -
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Residues in contact with LEU 696 (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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14A VAL* 4.8 2.2 - - + -
97A ALA* 3.5 34.5 - - + +
100A TYR* 3.7 19.5 - - + -
101A SER* 4.1 7.2 - - - +
671A LEU* 3.8 29.2 - - + -
672A ILE 3.9 18.4 - - - +
673A VAL* 3.6 21.4 - - + +
692A SER 2.9 16.1 + - - +
693A ALA* 3.6 5.2 - - - +
695A GLY* 1.3 73.2 - - - +
697A ILE* 1.3 65.7 + - - +
699A SER* 2.4 25.5 + - - +
700A PHE* 3.4 14.4 - - + -
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Residues in contact with ILE 697 (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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67A PHE* 3.6 59.9 - - + -
72A PRO* 4.1 6.5 - - + -
93A LEU* 3.6 37.5 - - + +
96A ALA* 3.9 7.9 - - + -
97A ALA 4.2 13.5 - - - +
100A TYR* 4.0 15.1 - - + -
693A ALA 2.9 19.9 + - - +
694A ALA* 3.7 6.7 - - - +
695A GLY 3.3 0.2 - - - -
696A LEU* 1.3 76.3 - - - +
698A ARG* 1.3 63.3 + - - +
700A PHE* 3.1 14.0 + - - +
701A SER* 3.1 13.0 + - - +
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Residues in contact with ARG 698 (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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71A ASP* 3.8 25.3 + - + +
72A PRO* 3.9 18.7 - - + +
73A ASP* 2.5 33.7 + - - +
689A TYR* 3.7 21.2 - - + -
690A GLU* 5.3 4.0 + - - -
694A ALA* 3.0 41.4 + - - +
695A GLY* 3.6 9.8 - - - +
696A LEU 3.3 0.2 - - - -
697A ILE* 1.3 76.9 - - - +
699A SER* 1.3 61.9 + - - +
701A SER* 3.2 19.0 + - - +
702A GLU* 3.2 14.5 + - + +
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Residues in contact with SER 699 (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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673A VAL* 4.1 5.8 - - - +
674A GLN 3.6 23.9 + - - -
676A ASN* 2.7 24.3 + - - -
689A TYR* 3.6 24.0 - - - -
695A GLY 3.1 9.9 + - - -
696A LEU* 2.4 30.0 + - - +
698A ARG* 1.3 77.0 - - - +
700A PHE* 1.3 66.5 + - - +
703A ARG* 3.3 17.3 + - - +
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Residues in contact with PHE 700 (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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42A TRP* 4.2 14.6 - + - -
46A LEU* 6.0 0.4 - - + -
60A TYR* 4.6 14.0 + + - +
68A ARG* 5.6 2.4 + - - -
100A TYR* 3.4 61.7 - + + -
101A SER* 4.6 2.7 - - - -
103A MET* 3.9 21.3 - - + -
696A LEU* 3.4 24.5 - - + -
697A ILE 3.1 7.6 + - - +
699A SER* 1.3 80.0 + - - +
701A SER* 1.3 65.7 + - - +
702A GLU 3.2 1.6 - - - -
703A ARG* 3.2 49.4 + - - +
704A PHE* 4.2 14.0 + + - -
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Residues in contact with SER 701 (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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67A PHE* 3.8 34.1 + - - +
68A ARG* 4.6 18.0 + - - +
72A PRO* 5.8 1.0 - - - +
100A TYR* 5.4 2.2 + - - -
697A ILE* 3.1 15.4 + - - +
698A ARG* 3.2 13.5 + - - -
700A PHE* 1.3 79.2 - - - +
702A GLU* 1.3 63.1 + - - +
703A ARG 3.4 1.0 + - - -
704A PHE 4.7 4.2 + - - -
705A PRO* 5.4 1.9 - - - +
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Residues in contact with GLU 702 (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 ASN* 3.7 7.9 + - - -
678A ARG* 3.0 43.9 + - - +
687A LEU* 4.3 12.4 - - + +
689A TYR* 2.9 43.4 + - - +
698A ARG* 3.2 9.7 + - - +
700A PHE 3.2 0.4 - - - -
701A SER* 1.3 80.6 - - - +
703A ARG* 1.3 61.2 + - - +
704A PHE 3.4 2.2 - - - -
705A PRO* 3.5 3.9 - - - +
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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