Contacts of the helix formed by residues 91 - 104 (chain A) in PDB entry 2Q9Q
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 91 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6A VAL* 3.8 22.4 - - + -
9A LEU* 3.7 22.5 + - + +
10A ALA* 3.3 30.1 - - + -
13A GLU* 3.5 33.9 - - + -
89A SER* 2.9 8.2 + - - +
90A PRO* 1.3 99.2 - - + +
92A TYR* 1.3 57.9 + - - +
93A MET 3.3 2.5 - - - -
94A GLU* 3.2 30.8 + - - +
95A LEU* 2.9 37.9 + - + +
149A THR* 4.5 0.7 - - - -
150A LEU* 4.4 16.0 - - + +
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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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65A TRP* 4.0 22.7 - + + -
71A LEU* 6.5 0.2 - - + -
87A MET* 3.1 51.1 - - + -
88A PRO* 4.6 3.4 - - + -
89A SER* 3.5 18.2 + - - +
91A TYR* 1.3 77.2 - - - +
93A MET* 1.3 83.5 + - + +
94A GLU* 5.6 0.2 - - - -
95A LEU 3.6 0.3 + - - -
96A THR* 2.7 33.1 + - - -
117A VAL* 3.8 23.6 - - + -
120A MET* 4.5 2.0 - - + -
121A TRP* 3.7 22.0 + - - -
124A ARG* 4.0 2.9 + - - -
149A THR* 4.2 15.0 - - + -
152A GLU* 2.8 34.7 + - + -
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Residues in contact with MET 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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91A TYR 3.3 0.8 - - - -
92A TYR* 1.3 104.8 - - + +
94A GLU* 1.3 69.0 + - - +
96A THR* 3.5 2.9 + - - -
97A LYS* 3.1 30.4 + - - +
117A VAL* 3.7 17.0 - - + +
118A LYS* 5.2 2.7 - - - -
121A TRP* 3.3 47.1 - - + -
151A MET* 4.7 6.5 - - + -
186D PHE* 4.2 19.7 - - + -
189D TRP* 4.1 20.0 - - + -
190D GLU* 5.1 7.2 - - - -
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Residues in contact with GLU 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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6A VAL* 2.9 30.3 - - + +
7A GLU* 4.0 19.3 - - + +
10A ALA* 3.5 25.8 - - + -
90A PRO 4.7 0.7 - - - +
91A TYR* 3.2 34.9 - - - +
92A TYR* 5.6 0.2 - - - -
93A MET* 1.3 81.4 + - - +
95A LEU* 1.3 57.4 + - + +
97A LYS* 3.4 0.3 + - - +
98A LEU* 2.9 37.6 + - + +
149A THR* 5.3 1.2 + - - +
151A MET* 3.5 18.5 + - + +
189D TRP* 3.9 21.3 - - + -
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Residues in contact with LEU 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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10A ALA* 4.4 9.2 - - + +
13A GLU* 4.6 12.1 - - + +
14A LEU 5.7 0.9 - - - +
15A VAL* 4.9 12.3 - - + -
46A LEU* 3.6 29.6 - - + -
63A PRO* 4.4 12.1 - - + -
65A TRP* 3.9 27.8 - - + +
66A MET* 4.1 3.6 - - + -
89A SER* 4.1 11.9 - - - +
91A TYR* 2.9 32.3 + - + +
92A TYR 4.1 2.7 - - - +
94A GLU* 1.3 74.0 - - - +
96A THR* 1.3 61.5 + - - +
98A LEU* 4.9 0.2 - - - -
99A LEU* 3.0 41.5 + - + +
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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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65A TRP* 4.1 3.5 - - - -
66A MET* 3.9 14.7 - - + +
92A TYR 2.7 22.9 + - - -
93A MET* 3.9 4.5 - - - -
95A LEU* 1.3 73.7 - - - +
97A LYS* 1.3 68.2 + - - +
100A LEU* 2.9 56.0 + - + +
113A ILE* 4.4 7.9 - - + +
114A ARG* 4.8 1.8 - - - -
117A VAL* 3.6 40.8 - - + +
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Residues in contact with LYS 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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7A GLU* 2.8 33.1 + - - +
93A MET* 3.1 19.8 + - + +
94A GLU 3.7 2.9 - - - +
96A THR* 1.3 78.0 - - - +
98A LEU* 1.3 74.8 + - + +
100A LEU* 5.1 0.9 - - - -
101A ASN* 3.0 48.2 + - - +
102A HIS* 5.7 1.8 + - - -
114A ARG* 5.1 4.0 - - - +
189D TRP* 3.7 46.4 + - + +
190D GLU* 4.4 18.2 - - + +
192D GLY* 4.8 11.3 + - - +
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Residues in contact with LEU 98 (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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7A GLU* 3.2 42.6 - - + +
11A GLU* 4.0 17.5 - - + +
46A LEU* 3.6 30.3 - - + -
50A ILE* 4.1 19.1 - - + +
94A GLU* 2.9 19.8 + - + +
95A LEU 4.5 0.9 - - - +
97A LYS* 1.3 91.2 - - + +
99A LEU* 1.3 57.1 + - - +
101A ASN 3.4 0.3 + - - -
102A HIS* 3.0 54.1 + - + +
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Residues in contact with LEU 99 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15A VAL* 5.4 5.6 - - + -
46A LEU* 4.2 20.0 - - + -
50A ILE* 4.6 4.3 - - + -
60A LEU* 3.8 35.4 - - + -
61A LEU 4.9 4.0 - - - +
63A PRO* 3.6 34.5 - - + -
66A MET* 3.6 11.7 - - + -
95A LEU* 3.0 33.4 + - + +
96A THR 4.3 0.2 - - - +
98A LEU* 1.3 76.5 - - - +
100A LEU* 1.3 55.5 + - - +
103A ALA* 2.7 39.9 + - + +
107A ILE* 3.5 18.2 - - + -
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Residues in contact with LEU 100 (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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66A MET* 4.7 1.6 - - - -
96A THR* 2.9 46.2 + - + +
99A LEU* 1.3 77.0 - - - +
101A ASN* 1.3 61.9 + - - +
104A SER* 3.3 25.9 + - - +
107A ILE* 4.0 22.7 - - + -
110A ALA* 3.8 31.4 - - + +
113A ILE* 4.4 8.5 - - + -
114A ARG* 3.4 59.8 + - + +
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Residues in contact with ASN 101 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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97A LYS* 3.0 44.3 + - + +
98A LEU* 3.9 2.9 - - - +
100A LEU* 1.3 79.3 + - - +
102A HIS* 1.3 77.4 + - + +
104A SER* 5.1 0.7 - - - -
114A ARG* 2.9 30.5 - - - +
190D GLU 5.0 4.2 - - - +
192D GLY 5.4 1.6 + - - -
193D GLN 4.4 25.3 + - - +
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Residues in contact with HIS 102 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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50A ILE* 3.6 35.8 - - + +
53A LYS* 3.3 23.6 + - + +
54A GLN* 3.7 28.5 + - + +
97A LYS* 5.7 1.4 + - - -
98A LEU* 3.0 40.3 + - + +
99A LEU* 5.3 0.2 - - - -
101A ASN* 1.3 96.7 + - + +
103A ALA* 1.3 61.9 + - + +
104A SER 3.9 0.4 - - - -
105A ASP* 5.7 0.2 - - - -
193D GLN 5.8 6.3 - - - -
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Residues in contact with ALA 103 (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 ILE* 6.5 0.2 - - + -
53A LYS* 3.9 9.0 - - + +
60A LEU* 3.6 35.7 - - + -
99A LEU* 2.7 23.1 + - + +
102A HIS* 1.3 76.5 - - + +
104A SER* 1.3 61.5 + - - +
105A ASP* 3.0 12.6 - - - +
106A ASN* 2.8 16.9 + - + -
107A ILE* 3.2 16.2 + - + +
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Residues in contact with SER 104 (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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99A LEU 3.5 3.4 + - - -
100A LEU* 3.3 21.6 + - - +
101A ASN 5.1 0.5 - - - -
103A ALA* 1.3 77.3 - - - +
105A ASP* 1.3 60.6 + - - +
106A ASN 3.0 0.2 - - - -
107A ILE* 2.9 27.5 - - - +
110A ALA* 4.0 23.5 - - - +
114A ARG* 6.2 1.1 - - - -
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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