Contacts of the strand formed by residues 106 - 115 (chain G) in PDB entry 3WTV
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 VAL 106 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5G VAL* 4.4 1.6 - - + -
8G GLN* 3.9 15.7 - - + +
11G LYS* 3.5 31.6 - - + -
12G PHE* 3.8 24.9 - - + +
18G PHE* 3.8 13.2 - - + -
102G ILE* 3.8 2.8 - - - +
103G LEU 2.7 42.8 + - - +
105G GLY* 1.3 77.6 - - - +
107G CYS* 1.3 63.6 + - - +
108G VAL* 3.1 22.3 + - + +
127G PHE* 3.9 13.7 - - + -
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Residues in contact with CYS 107 (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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4G VAL* 4.1 6.5 - - - -
8G GLN* 3.2 30.6 - - - +
101G MET 3.5 7.0 - - - +
102G ILE* 4.2 5.4 - - - +
105G GLY 4.2 0.2 - - - -
106G VAL* 1.3 69.9 - - - +
108G VAL* 1.3 61.1 + - - +
127G PHE* 3.7 10.1 - - - -
128G ASP* 3.0 22.9 + - + +
131G ARG* 3.0 50.5 - - + +
132G ALA* 3.8 13.0 - - - +
135G GLU* 4.1 7.4 - - - -
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Residues in contact with VAL 108 (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 PHE* 3.9 13.5 - - + -
18G PHE* 4.3 8.7 - - + -
100G PRO* 3.5 3.1 - - - +
101G MET* 2.9 35.5 + - + +
103G LEU* 4.5 7.6 - - + -
106G VAL* 3.1 34.5 + - + +
107G CYS* 1.3 75.7 - - - +
109G ILE* 1.3 76.2 + - - +
110G TRP 4.3 0.2 - - - -
125G LEU* 3.5 26.2 - - + -
126G GLU 2.9 33.0 - - - +
127G PHE* 4.7 0.4 - - - -
128G ASP* 3.8 2.1 - - - +
131G ARG* 6.0 0.5 - - - -
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Residues in contact with ILE 109 (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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98G LYS* 3.9 43.7 - - + +
99G ALA 3.8 8.1 - - - +
100G PRO* 4.4 7.9 - - + -
108G VAL* 1.3 80.9 - - - +
110G TRP* 1.3 62.5 + - - +
111G LYS* 3.7 15.7 + - + -
124G CYS 3.9 0.2 - - - +
125G LEU* 3.5 3.6 - - - -
126G GLU* 2.7 45.9 + - + +
128G ASP* 3.1 41.7 - - + +
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Residues in contact with TRP 110 (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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27G ILE* 3.6 26.5 - - + -
55G ILE* 3.5 31.7 + - + +
57G PHE* 3.3 37.4 - + - -
64G LEU* 4.5 5.5 - - + +
66G LEU* 3.3 41.6 - - + +
68G PHE* 4.2 6.1 - + - -
97G LEU* 3.7 29.6 - - + -
98G LYS* 3.1 6.1 - - - -
99G ALA 2.8 44.6 + - - +
101G MET* 3.6 13.8 - - + +
109G ILE* 1.3 71.3 - - - +
111G LYS* 1.3 68.9 + - - +
112G GLY* 4.1 11.0 - - - -
123G GLY* 5.0 0.2 - - - -
124G CYS 3.7 7.0 + - - +
125G LEU* 3.8 12.1 - - + +
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Residues in contact with LYS 111 (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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97G LEU 3.5 4.5 - - - +
98G LYS* 3.9 41.8 - - + +
109G ILE* 3.7 14.0 + - + +
110G TRP* 1.3 81.5 - - - +
112G GLY* 1.3 59.6 + - - +
123G GLY* 3.2 1.9 - - - -
124G CYS* 2.8 40.8 + - - +
126G GLU* 3.6 38.2 + - - +
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Residues in contact with GLY 112 (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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96G TYR* 3.5 5.7 - - - +
97G LEU* 2.7 43.3 + - - +
110G TRP* 4.1 13.2 - - - -
111G LYS* 1.3 76.2 - - - +
113G TRP* 1.3 60.4 + - - -
122G MET 3.3 13.2 - - - -
123G GLY* 3.8 3.4 - - - -
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Residues in contact with TRP 113 (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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24G GLU* 4.8 5.2 + - - -
27G ILE* 3.6 0.7 - - - +
94G LYS* 3.4 44.9 - - + -
95G VAL 3.0 13.0 - - - +
96G TYR* 3.9 37.7 + + + -
97G LEU* 5.6 0.2 - - - -
112G GLY* 1.3 76.4 - - - +
114G ILE* 1.3 77.8 + - - +
115G ASP* 4.2 9.2 - - + -
118G ARG* 6.0 2.5 - - - -
120G ASP* 4.1 6.5 - - - -
121G GLY* 3.5 17.2 - - - -
122G MET* 3.0 74.7 + - + +
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Residues in contact with ILE 114 (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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27G ILE* 3.6 13.7 - - + -
29G TYR 5.3 3.6 - - - +
44G PHE* 3.5 40.4 - - + -
55G ILE* 3.4 35.7 - - + -
94G LYS* 3.4 0.5 - - - -
95G VAL* 3.0 31.6 + - + +
97G LEU* 4.0 10.5 - - + -
113G TRP* 1.3 87.7 - - - +
115G ASP* 1.3 70.3 + - - +
116G LEU 3.2 2.4 + - - -
119G LEU* 3.6 9.6 - - - -
120G ASP* 3.2 26.9 - - - +
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Residues in contact with ASP 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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93G GLY* 3.4 16.0 - - - +
94G LYS* 4.4 9.3 - - + +
113G TRP* 4.1 9.9 - - + -
114G ILE* 1.3 69.7 - - - +
116G LEU* 1.3 55.3 + - - +
117G HIS* 2.5 51.3 + - - +
118G ARG* 3.1 34.6 + - + +
119G LEU* 2.9 24.8 + - - -
120G ASP 2.8 16.3 + - - +
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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