Contacts of the strand formed by residues 114 - 124 (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 CYS 114 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9G MET* 4.4 0.2 - - - -
10G HIS* 3.7 25.8 - - + -
11G MET* 4.3 2.9 - - - -
12G LYS* 4.6 10.5 - - - -
110G LEU* 3.2 11.0 - - - +
111G GLN* 2.6 42.6 + - - +
112G ASP 3.1 3.7 - - - +
113G GLY* 1.3 81.5 - - - +
115G LEU* 1.3 73.5 + - - +
116G ILE* 3.6 13.9 + - + +
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Residues in contact with LEU 115 (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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5G ILE* 4.3 1.1 - - + -
9G MET* 3.8 20.0 - - + -
10G HIS 3.1 11.5 + - - +
11G MET* 3.2 4.5 - - + +
12G LYS 2.8 27.5 + - - +
34G PRO* 5.9 1.1 - - + -
68G THR* 4.4 12.3 - - + +
69G PHE* 3.4 38.8 - - + -
84G PHE* 3.5 36.6 - - + -
108G THR* 4.7 2.9 - - + -
109G SER 3.4 3.8 - - - +
110G LEU* 3.6 17.7 - - + -
114G CYS* 1.3 74.7 - - - +
116G ILE* 1.3 59.6 + - - +
117G TYR* 3.8 21.1 - - + +
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Residues in contact with ILE 116 (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* 3.5 32.3 - - + +
14G TYR* 4.0 26.0 - - + +
107G ASP* 3.5 4.5 - - - +
109G SER* 2.6 47.8 + - - +
111G GLN* 4.6 15.7 - - + -
114G CYS* 4.1 16.8 - - + +
115G LEU* 1.3 74.6 - - - +
117G TYR* 1.3 64.5 + - - +
118G ASN* 4.1 12.2 + - - +
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Residues in contact with TYR 117 (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* 4.0 17.3 - - + -
12G LYS 2.8 18.1 + - - +
13G LEU* 3.2 27.9 - - + -
14G TYR* 2.7 36.2 + - - +
41G MET* 4.8 3.4 - - + -
62G PHE 4.0 11.0 - - - -
66G SER* 2.5 39.0 + - - -
67G LYS 5.8 0.4 - - - -
68G THR* 4.6 3.4 + - - -
69G PHE* 3.6 15.9 - - - -
88G PHE* 5.8 0.4 - + - -
106G GLN* 3.3 25.1 - - - +
107G ASP 3.5 2.2 - - - -
108G THR* 3.6 28.0 - - + -
115G LEU* 3.8 20.5 - - + +
116G ILE* 1.3 80.3 - - - +
118G ASN* 1.3 57.8 + - - +
119G VAL* 4.2 1.1 - - + -
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Residues in contact with ASN 118 (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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14G TYR* 3.3 32.0 + - - +
105G THR 3.9 0.7 - - - +
106G GLN* 3.2 2.9 - - - -
107G ASP* 2.9 46.6 + - + +
116G ILE* 4.1 11.1 + - - +
117G TYR* 1.3 75.1 - - - +
119G VAL* 1.3 62.6 + - - +
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Residues in contact with VAL 119 (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* 4.1 19.7 - - + -
14G TYR 2.9 9.8 + - - +
15G MET* 3.5 15.5 - - + -
16G GLU* 3.2 23.4 + - - +
61G SER 3.6 21.5 - - - +
90G TRP* 4.4 8.1 - - + -
104G ALA* 4.5 0.2 - - + -
105G THR 3.3 12.8 - - - +
106G GLN* 3.3 28.9 - - + +
118G ASN* 1.3 74.6 - - - +
120G LYS* 1.3 70.8 + - - +
121G ILE* 4.0 21.3 - - + -
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Residues in contact with LYS 120 (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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18F THR* 5.5 0.9 - - - +
122F ARG* 3.4 36.5 - - - +
16G GLU* 2.9 46.2 + - + +
104G ALA* 3.2 6.1 - - - +
105G THR* 2.8 41.9 + - - +
118G ASN 6.0 0.2 - - - -
119G VAL* 1.3 76.8 - - - +
121G ILE* 1.3 61.6 + - - +
122G ARG* 6.1 2.0 - - - +
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Residues in contact with ILE 121 (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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122F ARG* 4.7 1.6 - - - -
15G MET* 3.7 31.0 - - + -
16G GLU 2.9 7.4 + - - +
17G GLY* 2.8 25.6 - - - -
18G THR 3.0 5.7 + - - +
19G VAL* 4.5 0.7 - - + -
24G PHE* 3.9 14.1 - - + -
58G LEU* 4.0 13.0 - - + -
61G SER* 3.2 36.3 - - - +
102G LEU* 3.8 32.1 - - + -
103G THR 3.8 2.0 - - - -
104G ALA* 3.7 15.0 - - + -
119G VAL* 4.0 6.1 - - + -
120G LYS* 1.3 75.4 - - - +
122G ARG* 1.3 72.8 + - - +
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Residues in contact with ARG 122 (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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103F THR* 3.7 30.5 + - - +
104F ALA 4.4 0.4 - - - -
105F THR* 2.9 42.9 + - + +
120F LYS* 3.5 52.6 - - - +
121F ILE 4.3 5.1 + - - +
122F ARG* 4.2 21.6 - - + +
17G GLY* 4.8 3.8 - - - -
18G THR* 3.1 39.5 + - - +
23G HIS* 6.1 0.4 - - - -
101G VAL 4.0 0.9 - - - +
103G THR* 3.1 37.9 + - - +
120G LYS* 6.1 1.6 - - - +
121G ILE* 1.3 84.2 + - - +
123G GLY* 1.3 59.3 + - - +
124G VAL* 4.3 1.1 + - + -
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Residues in contact with GLY 123 (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* 4.9 2.8 - - - +
18G THR 2.7 14.0 + - - +
19G VAL* 3.3 7.3 - - - +
20G ASN* 3.0 25.0 + - - -
101G VAL 3.2 10.1 - - - -
102G LEU* 4.1 9.8 - - - +
122G ARG* 1.3 74.2 - - - +
124G VAL* 1.3 66.7 + - - +
126G PHE* 4.0 12.6 - - - -
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Residues in contact with VAL 124 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91F GLU* 3.9 24.2 - - + -
92F ARG 3.9 15.5 - - - +
93F VAL* 3.6 36.1 - - + +
103F THR* 3.7 21.1 - - + -
104F ALA 4.1 0.7 - - - +
105F THR* 4.0 16.4 - - + -
20G ASN* 3.5 5.4 - - - -
101G VAL* 2.8 37.3 + - + +
122G ARG* 4.7 0.7 - - + -
123G GLY* 1.3 79.4 - - - +
125G ASN* 1.3 66.9 + - + +
126G PHE* 3.2 7.5 + - - -
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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