Contacts of the strand formed by residues 9 - 19 (chain G) in PDB entry 3BXB
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 MET 9 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4G LEU 4.3 2.9 - - - +
5G ILE* 3.5 24.5 - - + -
6G THR* 3.1 37.7 - - - +
8G ASN* 1.3 71.6 - - - +
10G HIS* 1.3 67.3 + - - +
31G GLU* 3.2 5.0 - - - +
32G GLY 3.0 32.2 + - - -
34G PRO* 4.0 19.1 - - + +
69G PHE* 3.8 11.5 - - + -
110G LEU* 3.5 32.1 - - + -
113G GLY* 3.6 23.1 - - - +
114G CYS* 4.4 1.3 - - - -
115G LEU* 3.8 17.9 - - + +
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Residues in contact with HIS 10 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8G ASN* 5.0 6.1 - - + +
9G MET* 1.3 85.2 - - - +
11G MET* 1.3 63.9 + - - +
30G GLY 3.3 7.7 + - - +
31G GLU* 3.9 25.6 + - + +
42G ARG* 5.4 2.2 + - - -
69G PHE* 5.0 0.2 - - - -
113G GLY 4.6 4.9 + - - +
114G CYS* 3.7 16.2 - - + -
115G LEU* 3.1 27.0 + - - +
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Residues in contact with MET 11 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10G HIS* 1.3 76.2 - - - +
12G LYS* 1.3 60.3 + - - +
29G GLU* 3.2 8.3 - - - +
30G GLY 2.9 32.1 + - - +
31G GLU* 3.5 17.5 - - - +
39G GLN* 3.8 23.1 - - + +
40G THR 3.3 26.9 - - - +
41G MET* 3.5 25.6 - - + -
66G SER* 3.7 13.7 - - - -
69G PHE* 3.2 28.0 - - + -
114G CYS* 4.3 2.5 - - - -
115G LEU* 3.2 16.2 - - + +
117G TYR* 4.0 15.3 - - + -
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Residues in contact with LYS 12 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11G MET* 1.3 74.9 - - - +
13G LEU* 1.3 62.7 + - - +
14G TYR* 3.8 27.4 - - + +
28G SER 3.5 3.6 - - - +
29G GLU* 2.6 45.0 + - + +
114G CYS* 4.9 5.4 - - - -
115G LEU 2.8 5.1 + - - +
116G ILE* 3.5 26.7 - - + -
117G TYR* 2.8 27.9 + - - +
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Residues in contact with LEU 13 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12G LYS* 1.3 79.5 - - - +
14G TYR* 1.3 75.4 + - - +
15G MET* 3.7 21.1 - - + +
26G CYS 4.2 3.4 - - - +
27G THR* 3.2 24.3 - - - -
28G SER* 2.8 27.8 + - - +
41G MET* 4.2 4.7 - - + -
61G SER 4.3 0.2 - - - +
62G PHE* 3.5 59.5 - - + +
117G TYR* 3.2 30.5 - - + +
119G VAL* 4.1 11.2 - - + -
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Residues in contact with TYR 14 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12G LYS* 3.8 29.0 - - + +
13G LEU* 1.3 84.4 - - - +
15G MET* 1.3 60.1 + - - +
16G GLU 4.4 0.2 + - - -
26G CYS 3.6 3.6 - - - +
27G THR* 4.1 17.3 - - + -
116G ILE* 4.0 23.6 - - + +
117G TYR 2.7 17.7 + - - +
118G ASN* 3.3 28.9 + - - +
119G VAL 2.9 25.5 + - - +
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Residues in contact with MET 15 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13G LEU* 3.7 5.1 - - + +
14G TYR* 1.3 74.5 - - - +
16G GLU* 1.3 62.8 + - - +
24G PHE* 3.8 21.1 - - + -
25G LYS* 3.1 8.5 - - - +
26G CYS* 2.7 49.4 + - + +
58G LEU* 4.7 5.4 - - - -
61G SER* 3.6 37.2 - - - +
62G PHE* 3.7 36.1 - - + -
119G VAL* 3.5 17.0 - - + +
121G ILE* 3.7 26.2 - - + -
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Residues in contact with GLU 16 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120F LYS* 5.4 3.7 + - - +
14G TYR 4.3 0.2 - - - -
15G MET* 1.3 79.9 - - - +
17G GLY* 1.3 61.1 + - - +
23G HIS* 2.7 35.6 + - + +
24G PHE 3.5 3.6 - - - -
25G LYS* 3.4 29.6 - - + -
119G VAL 3.2 5.7 + - - -
120G LYS* 2.9 40.9 + - + +
121G ILE* 2.9 23.1 + - - +
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Residues in contact with GLY 17 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16G GLU* 1.3 79.7 - - - +
18G THR* 1.3 67.6 + - - -
23G HIS* 3.2 6.4 - - - -
24G PHE* 3.0 44.5 + - - -
120G LYS* 6.1 0.2 - - - -
121G ILE 2.8 15.7 - - - -
122G ARG* 4.8 5.8 - - - -
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Residues in contact with THR 18 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105F THR* 4.5 10.5 + - + +
120F LYS* 5.0 2.8 + - - -
17G GLY* 1.3 76.0 + - - -
19G VAL* 1.3 61.0 + - - +
21G ASN* 3.5 17.3 - - - +
22G HIS 3.3 29.2 - - - +
23G HIS* 3.9 14.9 - - + +
24G PHE* 3.7 0.8 - - - -
121G ILE 3.0 5.8 + - - +
122G ARG* 3.1 34.8 + - - +
123G GLY 2.7 30.9 + - - -
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Residues in contact with VAL 19 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18G THR* 1.3 78.6 - - - +
20G ASN* 1.3 74.7 + - - +
21G ASN 3.3 0.7 - - - -
22G HIS* 2.9 23.9 + - - +
24G PHE* 4.0 8.1 - - + -
53G PHE* 3.6 46.0 - - + -
57G ILE* 4.1 9.2 - - + -
58G LEU* 4.6 0.9 - - + -
102G LEU* 4.0 24.5 - - + -
121G ILE* 4.5 2.2 - - + -
123G GLY 3.3 4.9 - - - +
126G PHE* 4.0 24.5 - - + -
133G MET* 4.6 3.6 - - - +
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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