Contacts of the helix formed by residues 101 - 117 (chain A) in PDB entry 7BQQ
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 101 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5A LYS* 5.4 0.9 - - - -
95A ALA* 5.2 0.2 - - - -
100A ILE* 1.3 76.3 - - - +
102A PRO* 1.3 65.6 - - - +
103A GLU* 3.3 26.5 - - - -
104A GLN* 2.9 30.2 + - - +
105A VAL* 3.2 12.6 + - - +
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Residues in contact with PRO 102 (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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2A ASP* 6.5 0.9 - - + -
5A LYS* 3.9 37.7 - - + +
6A LEU* 4.3 13.9 - - + +
9A VAL* 3.6 30.9 - - + +
95A ALA* 5.3 2.4 - - + -
100A ILE 4.6 1.6 - - - +
101A SER* 1.3 83.3 - - - +
103A GLU* 1.3 67.1 + - - +
105A VAL* 3.3 11.2 + - + +
106A LYS* 2.9 28.9 + - - +
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Residues in contact with GLU 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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5A LYS* 2.8 40.4 + - - +
101A SER* 3.3 23.5 - - - -
102A PRO* 1.3 73.9 - - - +
104A GLN* 1.3 57.2 + - + +
105A VAL 3.4 0.2 - - - -
106A LYS* 3.4 22.5 - - + +
107A LYS* 3.1 23.7 + - - +
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Residues in contact with GLN 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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39A MET* 3.7 20.0 - - - +
43A ASN* 4.8 8.9 - - - +
45A GLU* 4.8 15.8 + - - +
46A VAL* 3.5 29.7 - - - +
100A ILE* 3.4 25.9 - - + +
101A SER* 2.9 25.1 + - - +
103A GLU* 1.3 76.4 - - + +
105A VAL* 1.3 58.0 + - - +
107A LYS* 3.2 24.7 + - + +
108A PHE 3.0 21.3 + - - -
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Residues in contact with VAL 105 (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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9A VAL* 3.4 20.9 - - + -
13A MET* 4.1 13.5 - - + -
91A ILE* 4.5 4.9 - - + -
94A PHE* 4.0 14.8 - - + -
95A ALA* 3.9 18.8 - - + -
100A ILE* 3.6 24.7 - - + -
101A SER 3.2 10.5 + - - +
102A PRO* 3.3 9.2 + - + +
104A GLN* 1.3 74.6 - - - +
106A LYS* 1.3 58.6 + - - +
108A PHE* 3.0 38.3 + - + +
109A ILE* 3.1 14.4 + - + +
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Residues in contact with LYS 106 (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 GLU* 2.8 54.6 + - - +
9A VAL* 4.1 7.3 - - + +
12A GLU* 3.6 29.6 - - + +
102A PRO* 2.9 11.6 + - - +
103A GLU* 3.4 28.0 - - + +
105A VAL* 1.3 74.8 - - - +
107A LYS* 1.3 54.7 + - - +
109A ILE* 3.3 23.6 - - - +
110A LYS* 4.3 4.7 + - - +
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Residues in contact with LYS 107 (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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39A MET* 4.7 8.5 - - + -
42A ASP* 4.9 11.9 + - - +
43A ASN* 5.5 7.6 + - - +
103A GLU 3.1 12.2 + - - +
104A GLN* 3.3 26.7 - - + +
105A VAL 3.1 0.4 - - - -
106A LYS* 1.3 74.7 - - - +
108A PHE* 1.3 66.0 + - - +
109A ILE 3.4 0.2 - - - -
110A LYS* 3.1 29.1 + - - +
111A ILE* 3.5 16.8 + - + +
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Residues in contact with PHE 108 (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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13A MET* 3.9 4.5 - - + -
32A VAL* 4.1 9.4 - - + -
35A ALA* 3.5 30.5 - - + -
36A LEU* 3.5 29.8 - - + -
39A MET* 3.6 27.6 - - + -
72A VAL* 3.7 37.2 - - + -
94A PHE* 4.5 2.9 - + - -
104A GLN 3.0 6.5 + - - +
105A VAL* 3.0 24.7 + - + +
107A LYS* 1.3 74.8 - - - +
109A ILE* 1.3 82.5 + - + +
111A ILE* 2.9 30.5 + - - +
112A MET* 3.0 23.6 + - + -
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Residues in contact with ILE 109 (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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9A VAL* 5.7 0.2 - - + -
12A GLU* 3.5 44.0 - - + +
13A MET* 4.0 17.9 - - + -
16A MET* 3.6 39.2 - - + +
105A VAL 3.1 11.9 + - - +
106A LYS* 3.3 20.9 - - - +
108A PHE* 1.3 92.6 - - + +
110A LYS* 1.3 63.9 + - + +
112A MET* 3.2 12.0 + - + +
113A ARG* 3.2 28.1 + - - +
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Residues in contact with LYS 110 (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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106A LYS 4.4 6.7 - - - +
107A LYS* 3.1 22.2 + - - +
109A ILE* 1.3 82.2 - - + +
111A ILE* 1.3 61.1 + - + +
113A ARG* 3.4 19.9 - - - +
114A GLU* 3.2 26.6 - - + +
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Residues in contact with ILE 111 (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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35A ALA* 4.0 19.7 - - - +
38A GLN* 3.7 39.9 - - + +
39A MET* 4.4 15.9 - - + -
42A ASP* 6.4 0.4 - - + -
107A LYS* 3.5 19.9 + - + +
108A PHE* 2.9 15.0 + - - +
110A LYS* 1.3 76.2 - - - +
112A MET* 1.3 63.9 - - - +
114A GLU* 3.0 9.5 + - + +
115A VAL* 3.0 26.9 + - + +
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Residues in contact with MET 112 (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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16A MET* 3.9 26.0 - - + -
20A MET* 3.7 27.1 - - - -
31A ILE* 4.4 13.0 - - + -
32A VAL* 4.7 7.4 - - + -
35A ALA* 3.7 22.6 - - + +
76A MET* 3.6 33.0 - - + -
108A PHE* 3.0 30.0 + - + +
109A ILE* 3.2 13.7 + - + +
111A ILE* 1.3 75.1 - - - +
113A ARG* 1.3 57.3 + - - +
115A VAL* 3.4 4.1 + - - +
116A GLN* 2.9 41.4 + - - +
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Residues in contact with ARG 113 (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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16A MET* 3.7 33.8 - - + +
19A ASN* 4.6 10.9 + - - +
109A ILE* 3.2 7.5 + - - +
110A LYS* 3.4 30.5 - - - +
112A MET* 1.3 77.8 - - - +
114A GLU* 1.3 66.9 + - + +
115A VAL 3.7 0.2 + - - -
116A GLN* 3.7 15.2 + - - +
117A ARG* 3.7 24.1 + - - +
124A GLU* 2.8 45.9 + - - +
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Residues in contact with GLU 114 (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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110A LYS* 3.2 19.1 - - + +
111A ILE* 3.0 13.1 + - + +
113A ARG* 1.3 81.2 - - + +
115A VAL* 1.3 57.4 + - - +
117A ARG* 2.8 63.2 + - - +
118A LYS* 3.7 21.4 - - - +
123A LEU* 5.5 0.5 - - - +
124A GLU* 5.1 3.9 - - - +
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Residues in contact with VAL 115 (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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31A ILE* 4.0 27.1 - - + +
34A ARG* 3.8 32.7 + - + +
35A ALA* 4.1 8.7 - - + +
111A ILE* 3.0 19.8 + - + +
112A MET* 3.5 15.7 - - - +
114A GLU* 1.3 75.2 - - - +
116A GLN* 1.3 63.1 + - - +
117A ARG 3.4 0.7 - - - -
118A LYS* 3.3 30.4 + - + +
119A GLU* 3.7 10.2 + - - +
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Residues in contact with GLN 116 (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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16A MET* 4.9 0.2 - - - +
19A ASN* 2.9 31.1 + - - +
20A MET* 3.4 42.4 - - + +
23A GLN* 4.0 7.4 - - - +
31A ILE* 3.8 27.1 - - + +
112A MET* 2.9 23.7 + - + +
113A ARG* 3.7 19.5 - - - +
115A VAL* 1.3 78.8 - - - +
117A ARG* 1.3 60.9 + - + +
118A LYS 3.4 0.2 + - - -
119A GLU* 3.5 20.6 + - - +
120A ASP* 4.7 2.6 + - - +
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Residues in contact with ARG 117 (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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113A ARG 3.8 10.5 - - - +
114A GLU* 2.8 48.4 + - - +
116A GLN* 1.3 79.0 - - - +
118A LYS* 1.3 62.3 + - - +
119A GLU 3.2 0.2 - - - -
120A ASP* 3.1 9.3 + - - +
121A GLY* 2.9 28.7 + - - -
122A SER* 2.8 54.4 + - - +
123A LEU* 3.7 34.0 - - - +
124A GLU* 4.3 18.7 - - + +
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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