Contacts of the helix formed by residues 87 - 97 (chain A) in PDB entry 4DTP
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 ASP 87 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10A GLN* 5.6 0.2 - - - +
85A MET* 3.2 28.1 - - - +
86A ASP* 1.3 79.6 + - - +
88A PHE* 1.3 64.6 + - - +
89A LYS* 2.8 41.0 + - - +
90A LEU* 3.2 22.9 + - + +
363A LYS* 2.6 34.9 + - - +
366A ASP* 5.9 0.2 - - - +
576A ARG* 6.0 0.2 - - - +
2T C 4.6 9.3 + - - +
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Residues in contact with PHE 88 (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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10A GLN* 3.9 19.3 + - - +
15A ILE* 4.7 1.3 - - - -
33A TYR* 3.7 7.4 - + + -
35A PRO* 3.6 24.7 - - + -
36A SER 5.7 0.2 - - - -
37A LEU* 4.4 12.6 - - + -
65A MET* 3.5 45.8 - - + -
68A ALA* 3.6 22.7 - - + -
69A SER* 3.6 26.5 - - - -
72A ILE* 4.8 3.6 - - + -
85A MET 3.8 16.4 - - - -
86A ASP* 3.3 19.9 + - - -
87A ASP* 1.3 73.1 + - - +
89A LYS* 1.3 57.9 + - - +
91A ALA* 3.1 10.1 + - + +
92A TYR* 2.8 27.1 + - - +
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Residues in contact with LYS 89 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A VAL* 4.0 26.7 - - + +
9A GLU* 5.1 2.2 - - - -
10A GLN* 4.1 30.1 + - + +
15A ILE* 4.1 13.0 - - + +
87A ASP* 2.8 35.0 + - - +
88A PHE* 1.3 77.2 - - - +
90A LEU* 1.3 62.2 + - + +
92A TYR* 3.5 7.8 - - - +
93A LEU* 2.9 34.3 + - - +
354A GLN* 3.7 38.4 - - + +
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Residues in contact with LEU 90 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A VAL* 6.5 0.2 - - + -
85A MET* 4.0 28.0 - - + -
87A ASP* 3.2 26.9 + - + +
89A LYS* 1.3 80.0 - - + +
91A ALA* 1.3 61.2 + - - +
93A LEU* 3.5 6.5 + - + +
94A SER* 3.0 29.1 + - - -
352A LYS* 3.6 22.4 - - - +
353A ILE* 3.9 18.8 - - + -
354A GLN* 4.9 4.5 - - + +
363A LYS* 3.8 26.0 - - + +
366A ASP* 4.7 2.0 - - - +
367A ALA* 4.0 19.7 - - + +
370A PHE* 3.6 7.8 - - + -
371A ASN* 5.2 1.6 + - - +
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Residues in contact with ALA 91 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A TYR* 3.3 19.3 - - + +
35A PRO* 5.9 1.1 - - + -
36A SER 6.1 2.5 - - - +
85A MET* 3.9 22.5 - - + +
87A ASP 3.5 2.2 + - - -
88A PHE* 3.1 13.8 + - + +
90A LEU* 1.3 78.0 - - - +
92A TYR* 1.3 58.5 + - - +
94A SER* 3.3 2.4 + - - -
95A ASP* 2.8 34.4 + - - -
370A PHE* 3.9 15.0 - - + -
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Residues in contact with TYR 92 (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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8A VAL* 3.9 11.2 - - + -
15A ILE* 3.7 35.4 - - + -
17A GLU* 2.6 39.7 + - + +
29A ARG* 3.6 12.0 + - - -
31A VAL* 3.7 29.0 - - + +
33A TYR* 3.5 35.4 + + + -
88A PHE 2.8 13.4 + - - +
89A LYS* 3.5 11.4 - - - +
90A LEU 3.3 0.2 - - - -
91A ALA* 1.3 75.1 - - - +
93A LEU* 1.3 61.8 + - + +
95A ASP* 3.2 2.1 + - - +
96A THR* 2.8 58.2 + - - +
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Residues in contact with LEU 93 (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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5A TYR* 3.7 51.1 - - + -
8A VAL* 3.8 33.7 - - + -
17A GLU* 4.9 0.2 - - - +
89A LYS 2.9 21.5 + - - +
90A LEU* 3.9 6.3 - - + +
92A TYR* 1.3 85.5 - - + +
94A SER* 1.3 58.6 + - - +
97A TYR* 2.9 43.9 + - + +
352A LYS* 3.6 31.4 - - + +
353A ILE* 4.1 6.5 - - - +
354A GLN 4.6 0.2 - - - +
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Residues in contact with SER 94 (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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90A LEU 3.0 18.3 + - - -
91A ALA 3.5 4.9 - - - -
93A LEU* 1.3 78.7 - - - +
95A ASP* 1.3 60.4 + - - +
97A TYR 3.9 0.2 - - - +
98A ASN* 3.7 18.9 + - - +
352A LYS* 4.6 5.7 + - - +
370A PHE* 3.5 14.3 - - - -
371A ASN* 2.7 29.8 + - - -
374A LYS* 2.9 35.7 + - - +
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Residues in contact with ASP 95 (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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33A TYR* 2.5 34.9 + - + +
91A ALA* 2.8 18.8 + - - +
92A TYR* 3.7 4.7 - - - +
94A SER* 1.3 73.7 - - - +
96A THR* 1.3 63.9 + - - +
98A ASN* 4.3 9.9 - - - +
374A LYS* 3.3 23.3 - - - +
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Residues in contact with THR 96 (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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17A GLU* 4.4 3.1 - - - +
29A ARG* 3.6 23.6 - - - +
92A TYR* 2.8 44.4 + - - +
95A ASP* 1.3 79.2 - - - +
97A TYR* 1.3 90.2 + - + +
98A ASN 3.6 1.7 + - - -
99A TYR* 4.5 6.4 + - - -
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Residues in contact with TYR 97 (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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3A GLU* 3.6 14.8 - - + -
4A PHE* 3.5 21.2 - - - -
5A TYR* 3.3 33.2 + + + -
17A GLU* 2.4 35.2 + - - -
19A TYR* 3.5 12.0 - - - +
29A ARG* 3.7 6.2 + - - -
93A LEU* 2.9 22.9 + - + +
94A SER 3.8 4.5 - - - +
96A THR* 1.3 97.0 - - + +
98A ASN* 1.3 55.3 - - - +
99A TYR* 2.9 38.1 + + + -
101A ILE* 3.9 24.2 - - + -
352A LYS* 3.0 22.7 + - + +
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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