Contacts of the helix formed by residues 76 - 85 (chain A) in PDB entry 2STT
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 76 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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55A LEU* 2.7 22.8 - - + +
58A PRO* 4.0 26.9 - - + -
61A VAL* 6.3 1.3 - - + -
62A ALA* 4.4 20.4 - - + +
74A MET 3.5 2.9 + - - -
75A ASN* 1.3 67.9 - - - +
77A GLU* 1.3 63.9 + - - +
78A LYS 2.9 2.9 - - - -
79A LEU* 2.7 45.0 + - + +
80A SER* 3.3 7.8 + - - -
99A ARG 5.5 1.3 - - - -
100A TYR* 5.4 11.4 - + - -
102A TYR* 2.5 46.9 + + - -
6B C 3.9 20.0 - - - -
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Residues in contact with GLU 77 (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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75A ASN* 3.1 17.7 - - + +
76A TYR* 1.3 81.4 - - - +
78A LYS* 1.3 52.4 + - - +
80A SER* 3.0 6.8 + - - +
81A ARG* 2.7 36.2 + - - +
5B G 3.0 29.3 + - + +
6B C 2.6 58.6 + - + +
7B C 3.7 21.6 + - - +
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Residues in contact with LYS 78 (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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65A TRP* 3.0 21.8 - - + +
69A LYS* 4.1 6.2 - - - +
74A MET* 3.9 17.7 - - + -
75A ASN* 2.9 30.8 + - - +
76A TYR 2.9 0.2 - - - -
77A GLU* 1.3 77.9 - - - +
79A LEU* 1.3 64.6 + - + +
81A ARG* 3.7 15.2 - - - +
82A GLY* 2.6 33.5 + - - -
83A LEU 5.8 0.6 - - - +
24C T 2.5 46.2 + - - -
25C T 2.8 41.7 - - + +
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Residues in contact with LEU 79 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A LEU* 5.6 1.8 - - + -
62A ALA* 5.8 3.4 - - + -
65A TRP* 3.2 72.0 - - + +
74A MET* 5.6 1.6 - - + -
75A ASN 5.0 2.9 - - - +
76A TYR* 2.7 47.6 + - + +
78A LYS* 1.3 84.7 - - + +
80A SER* 1.3 58.2 + - - +
83A LEU* 2.4 56.9 + - + +
102A TYR* 4.3 6.3 - - + +
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Residues in contact with SER 80 (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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76A TYR* 3.3 7.8 + - - -
77A GLU* 3.0 12.8 + - - -
79A LEU* 1.3 78.5 - - - +
81A ARG* 1.3 60.8 + - - +
83A LEU* 4.8 0.4 - - - -
84A ARG* 2.8 34.4 + - - +
99A ARG 5.7 0.5 + - - -
102A TYR* 4.0 13.5 + - - -
6B C 4.1 14.8 + - - -
7B C 2.9 43.3 + - - +
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Residues in contact with ARG 81 (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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75A ASN* 5.4 6.2 + - - +
77A GLU 2.7 19.8 + - - +
78A LYS* 3.7 13.4 - - - +
80A SER* 1.3 75.5 - - - +
82A GLY* 1.3 59.6 + - - +
84A ARG* 4.1 9.6 + - - +
85A TYR* 3.6 17.2 + - - +
7B C 3.7 26.8 - - + +
8B G 3.6 21.5 - - + +
9B G 4.3 5.9 - - - +
25C T 4.2 26.4 - - + +
26C C 3.1 45.8 + - - +
27C C 3.1 25.3 - - - +
28C G 4.5 9.1 + - - +
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Residues in contact with GLY 82 (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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78A LYS* 2.6 22.6 + - - -
81A ARG* 1.3 74.5 - - - +
83A LEU* 1.3 63.9 + - - -
84A ARG 3.3 0.2 - - - -
85A TYR* 3.2 6.6 + - - +
86A TYR* 3.2 17.3 + - - +
24C T 4.2 36.7 + - - +
25C T 4.4 7.4 - - - +
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Residues in contact with LEU 83 (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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27A LEU* 4.5 10.8 - - + -
31A LEU* 4.8 3.8 - - + -
65A TRP* 4.2 17.9 - - + -
78A LYS* 4.0 1.2 + - - +
79A LEU* 2.4 59.7 + - + +
80A SER* 4.8 0.9 - - - -
82A GLY* 1.3 71.4 - - - -
84A ARG* 1.3 54.4 + - - +
86A TYR* 2.6 39.3 + - + +
87A TYR* 5.2 0.9 - - + -
92A ILE* 3.6 46.0 - - + +
102A TYR* 4.3 18.6 - - + -
24C T 4.9 0.6 + - - -
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Residues in contact with ARG 84 (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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80A SER* 2.8 25.3 + - - +
81A ARG* 4.1 12.9 + - - +
83A LEU* 1.3 80.6 - - - +
85A TYR* 1.3 88.9 + - - +
86A TYR 2.8 6.1 + - - -
87A TYR* 3.2 35.5 - - + +
94A LYS* 3.8 29.4 - - + +
7B C 4.2 15.3 - - - +
8B G 2.6 54.0 + - - +
9B G 4.4 18.0 + - - -
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Residues in contact with TYR 85 (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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81A ARG 3.6 12.9 + - - +
82A GLY* 3.2 10.5 + - - +
83A LEU 3.2 0.6 - - - -
84A ARG* 1.3 105.2 - - - +
86A TYR* 1.3 56.4 + - - +
87A TYR* 3.0 10.0 + - - +
88A ASP* 3.8 20.0 - - - +
9B G 5.5 8.7 - + - -
10B A 5.6 10.8 - - - -
11B A 5.2 4.5 + - - -
23C C 4.5 21.1 + + - -
24C T 4.2 28.5 - - + -
25C T 6.1 0.2 - - - +
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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