Contacts of the strand formed by residues 110 - 121 (chain E) in PDB entry 2VT5
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 ARG 110 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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89E PHE* 3.8 6.4 - - - +
91E THR 3.3 3.6 - - - +
92E CYS* 4.1 13.5 - - + -
104E ILE* 3.8 12.5 - - - +
105E VAL* 2.6 33.1 + - + +
106E GLU* 3.5 4.0 - - - +
107E PRO* 3.3 43.8 + - - +
108E GLU 3.5 1.5 - - - +
109E LYS* 1.3 78.0 - - - +
111E GLY* 1.3 61.4 + - - +
146E GLU* 3.2 36.2 + - - -
147E PRO* 3.4 27.6 - - - +
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Residues in contact with GLY 111 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29E GLU* 3.2 13.2 - - - -
89E PHE 3.3 11.8 + - - -
90E ALA 3.5 6.1 - - - -
91E THR 2.7 10.8 + - - +
92E CYS* 3.2 25.5 - - - +
109E LYS 3.6 1.2 + - - -
110E ARG* 1.3 75.7 - - - +
112E LYS* 1.3 59.1 + - - -
113E TYR 3.4 2.7 - - - -
141E LYS* 5.6 0.2 - - - +
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Residues in contact with LYS 112 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27E THR* 3.2 19.1 + - - +
29E GLU* 2.6 56.1 + - - +
92E CYS* 4.3 5.6 - - - -
111E GLY* 1.3 71.7 - - - -
113E TYR* 1.3 77.2 + - + +
140E ARG* 3.5 43.0 - - + +
141E LYS* 3.0 32.0 + - + +
1337E ROK 5.5 0.8 + - - -
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Residues in contact with TYR 113 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29E GLU* 4.0 8.5 - - + -
30E LEU* 3.6 42.0 + - + +
33E LEU* 3.5 24.9 - - + -
90E ALA 3.0 23.6 + - - +
91E THR* 3.1 6.8 - - - -
92E CYS* 2.8 28.2 + - - -
93E VAL 3.7 0.2 + - - -
111E GLY 3.4 0.4 - - - -
112E LYS* 1.3 105.7 + - + +
114E VAL* 1.3 62.9 + - - +
138E ILE* 3.7 13.5 - - + -
139E TYR 3.3 15.5 - - - +
140E ARG* 4.0 28.1 + - + -
160E VAL* 4.1 21.3 - - + +
1337E ROK 4.4 6.4 + - - -
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Residues in contact with VAL 114 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92E CYS* 4.1 10.5 - - - -
93E VAL* 3.3 32.5 - - + +
95E VAL* 5.6 0.2 - - + -
113E TYR* 1.3 75.9 - - - +
115E VAL* 1.3 68.3 + - - +
116E CYS* 4.2 3.1 - - - -
137E GLY 3.8 0.5 - - - +
138E ILE* 3.4 2.8 - - - +
139E TYR* 2.6 51.8 + - + +
140E ARG 4.7 0.7 - - - -
141E LYS* 4.1 19.1 - - + +
151E ASP* 4.0 14.1 - - + +
152E ALA* 3.8 33.7 - - + -
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Residues in contact with VAL 115 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33E LEU* 4.0 21.8 - - + -
37E LEU* 5.3 2.5 - - + -
85E LEU* 3.8 19.7 - - + -
91E THR* 3.8 28.5 - - + -
93E VAL 3.1 6.9 + - - -
94E LEU* 3.5 13.8 - - + -
95E VAL 2.8 26.3 + - - +
114E VAL* 1.3 79.8 - - - +
116E CYS* 1.3 69.3 + - - +
117E PHE* 4.0 10.9 - - + -
136E PHE* 4.6 10.5 - - + -
137E GLY 3.4 8.3 - - - +
138E ILE* 4.3 12.1 - - + -
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Residues in contact with CYS 116 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95E VAL* 3.3 17.7 - - + +
114E VAL* 4.8 1.1 - - - -
115E VAL* 1.3 76.4 - - - +
117E PHE* 1.3 62.4 + - - +
136E PHE* 3.2 2.9 - - - +
137E GLY 2.7 39.4 + - - +
139E TYR* 4.2 21.8 - - + -
152E ALA* 3.9 13.9 - - - -
278E LEU* 3.5 50.5 - - + +
279E TYR* 3.8 5.5 - - + +
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Residues in contact with PHE 117 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37E LEU* 6.0 0.2 - - + -
78E ASN* 3.4 20.0 - - - -
81E VAL* 3.6 39.9 - - + -
82E MET* 3.4 39.5 - - + -
85E LEU* 3.9 16.8 - - + -
94E LEU* 4.4 9.6 - - + -
95E VAL 2.8 15.7 + - - +
96E SER* 3.4 12.8 - - - -
97E GLU 3.3 22.2 + - - -
115E VAL* 4.0 6.5 - - + -
116E CYS* 1.3 78.3 - - - +
118E ASP* 1.3 58.9 + - - +
119E PRO* 3.7 17.3 - - + -
134E THR* 5.4 2.7 - - + -
135E ILE 3.1 13.2 - - - +
136E PHE* 4.0 10.5 - - + -
279E TYR* 3.4 12.4 - - - +
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Residues in contact with ASP 118 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97E GLU* 3.5 29.8 - - - +
117E PHE* 1.3 73.7 - - - +
119E PRO* 1.3 73.6 - - - +
120E LEU 3.3 10.2 + - - +
121E ASP* 2.9 40.5 + - + +
134E THR* 3.4 2.8 - - - -
135E ILE* 2.8 32.4 + - + +
279E TYR* 3.9 21.2 - - + +
280E GLU* 3.7 8.5 - - - +
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Residues in contact with PRO 119 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44E ILE* 4.1 2.6 - - - +
74E ASP* 4.4 3.1 - - + +
77E SER* 3.7 14.5 - - - +
78E ASN* 3.5 49.1 - - + +
81E VAL* 4.5 2.5 - - + -
96E SER* 3.7 15.9 - - - +
97E GLU* 4.4 4.7 - - + -
98E GLU* 4.0 10.1 - - + -
117E PHE* 3.7 15.4 - - + +
118E ASP* 1.3 91.2 - - - +
120E LEU* 1.3 61.2 + - - +
134E THR* 2.7 31.1 + - + +
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Residues in contact with LEU 120 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44E ILE* 4.0 11.0 - - + -
48E VAL* 3.9 19.1 - - + -
73E LEU* 3.9 27.6 - - + -
74E ASP* 4.2 9.0 - - + +
77E SER* 3.7 20.0 - - - +
118E ASP* 3.8 6.0 + - - +
119E PRO* 1.3 87.4 - - - +
121E ASP* 1.3 62.6 + - - +
122E GLY 3.5 2.1 + - - -
123E SER* 3.6 33.5 + - - -
126E ILE* 4.2 5.2 - - + -
132E VAL* 3.8 24.5 - - + -
133E GLY 3.2 7.4 - - - +
167E TYR* 4.1 3.8 - - + -
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Residues in contact with ASP 121 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118E ASP* 2.9 23.9 + - + +
120E LEU* 1.3 73.6 - - - +
122E GLY* 1.3 63.3 + - - +
132E VAL* 3.5 7.4 - - - +
133E GLY 2.5 37.4 + - - +
135E ILE* 3.7 16.3 - - + +
247E SER* 4.0 1.7 + - - -
248E MET* 3.7 25.8 + - - +
249E VAL* 4.0 14.5 + - + +
280E GLU* 2.4 34.0 - - - +
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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