Contacts of the helix formed by residues 87 - 97 (chain A) in PDB entry 2Y8P
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 THR 87 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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84A LYS* 3.0 35.3 + - + +
86A SER* 1.3 90.8 - - - +
88A SER* 1.3 73.1 + - - -
89A GLY 3.2 0.4 - - - -
90A ARG* 3.2 7.1 + - - +
91A ASP* 2.9 29.8 + - - +
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Residues in contact with SER 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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82A GLN 4.9 0.7 + - - -
83A LEU* 3.7 15.3 - - - +
84A LYS* 3.2 21.0 + - - +
87A THR* 1.3 83.7 + - - +
89A GLY* 1.3 65.5 + - - +
91A ASP* 3.2 2.9 + - - +
92A VAL* 3.0 28.5 + - - +
120A TYR* 3.6 43.2 + - - -
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Residues in contact with GLY 89 (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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83A LEU* 4.6 6.0 - - - +
84A LYS 2.9 16.7 + - - +
85A ALA* 3.6 4.9 - - - -
88A SER* 1.3 80.7 + - - +
90A ARG* 1.3 60.3 + - - +
92A VAL 3.2 0.5 + - - -
93A TYR* 3.1 21.1 + - - -
102A PRO* 3.8 13.2 - - - -
116A MET* 3.6 26.8 - - - +
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Residues in contact with ARG 90 (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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85A ALA 2.9 17.3 + - - +
86A SER* 2.6 35.4 + - - +
87A THR* 3.2 12.0 + - - +
89A GLY* 1.3 75.8 - - - +
91A ASP* 1.3 55.6 + - - +
93A TYR* 3.0 5.0 + - - +
94A ARG* 2.8 38.0 + - + +
100A GLY 4.1 14.4 - - - +
101A GLU* 3.5 25.1 + - + +
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Residues in contact with ASP 91 (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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87A THR 2.9 18.9 + - - +
88A SER* 3.2 11.7 + - - +
90A ARG* 1.3 79.5 + - - +
92A VAL* 1.3 55.9 + - - +
94A ARG* 3.4 17.2 + - - +
95A ARG* 3.0 28.1 + - - +
120A TYR* 3.8 26.6 + - + -
123A ILE* 3.7 12.3 - - + +
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Residues in contact with VAL 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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83A LEU* 4.8 0.7 - - + -
88A SER 3.0 14.5 + - - +
89A GLY 3.6 7.6 - - - +
90A ARG 3.2 0.2 - - - -
91A ASP* 1.3 73.6 - - - +
93A TYR* 1.3 68.8 + - + +
95A ARG* 3.1 4.8 + - + +
96A MET* 3.0 32.5 + - + +
98A TRP* 5.4 2.5 - - + -
116A MET* 3.6 47.1 - - + +
119A ALA* 3.8 20.9 - - + -
120A TYR* 3.9 21.1 - - + +
123A ILE* 4.0 9.0 - - + -
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Residues in contact with TYR 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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89A GLY 3.1 16.0 + - - +
90A ARG 3.0 6.6 + - - +
92A VAL* 1.3 76.8 - - + +
94A ARG* 1.3 61.8 + - - +
96A MET 3.3 1.6 + - - -
97A GLY 3.1 4.0 + - - -
98A TRP* 2.8 71.3 + + + +
99A SER 3.5 14.8 - - - -
100A GLY 3.4 27.4 - - - +
101A GLU* 3.7 16.4 - - - -
102A PRO* 3.7 11.7 - - + +
106A GLU* 3.5 21.8 + - - -
112A ARG* 5.5 3.5 + - - -
116A MET* 3.9 24.8 - - + -
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Residues in contact with ARG 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 ARG* 2.8 21.1 + - + +
91A ASP* 3.8 17.6 + - - +
93A TYR* 1.3 78.3 - - - +
95A ARG* 1.3 67.1 + - - +
97A GLY* 3.1 13.1 + - - -
98A TRP 4.2 6.9 + - - -
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Residues in contact with ARG 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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50A TRP* 4.0 37.3 - - + -
91A ASP 3.0 14.9 + - - +
92A VAL* 3.1 9.4 + - - +
94A ARG* 1.3 82.8 - - - +
96A MET* 1.3 62.9 + - + +
119A ALA* 5.9 0.4 - - + -
122A ASN* 4.8 8.3 + - - -
123A ILE* 3.5 26.9 - - + +
126A THR* 5.8 1.2 + - - -
48B ALA 5.1 0.4 + - - -
49B ALA* 2.8 39.9 + - - +
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Residues in contact with MET 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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50A TRP* 3.6 31.9 - - + -
92A VAL* 3.0 26.3 + - + +
93A TYR 3.8 1.1 - - - +
94A ARG 3.2 0.4 - - - -
95A ARG* 1.3 80.7 - - + +
97A GLY* 1.3 61.0 + - - +
98A TRP* 3.6 57.9 + - + +
46B ALA* 4.9 2.4 - - - -
49B ALA* 3.3 15.8 - - - +
50B TRP* 4.0 24.1 + - + +
96B MET* 3.8 27.8 - - - -
98B TRP* 5.2 2.9 - - + -
115B SER* 4.2 7.4 + - - +
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Residues in contact with GLY 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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93A TYR 3.1 2.8 + - - -
94A ARG* 3.1 12.8 + - - -
95A ARG 3.2 1.4 + - - -
96A MET* 1.3 79.8 - - - +
98A TRP* 1.3 63.7 + - - +
42B ILE* 5.3 3.3 - - - +
45B LYS* 3.5 50.7 + - - +
46B ALA* 4.6 3.5 + - - +
49B ALA* 4.2 0.7 - - - -
111B GLU* 4.5 5.4 - - - +
115B SER* 5.9 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