Contacts of the strand formed by residues 146 - 157 (chain E) in PDB entry 1VHA
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 GLY 146 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11E HIS 3.2 14.1 - - - -
13E PHE* 3.5 12.8 - - - -
101E ALA* 5.3 0.2 - - - -
140E PHE* 3.7 5.5 + - - -
141E THR* 3.4 27.2 - - - +
144E GLN* 3.2 2.5 - - - -
145E GLU* 1.3 82.4 + - - +
147E ILE* 1.3 69.1 + - - +
138F LEU* 4.1 8.0 - - - +
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Residues in contact with ILE 147 (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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10E VAL* 3.4 4.7 - - - +
11E HIS* 2.9 39.3 + - + +
13E PHE* 3.6 26.2 - - + -
38E GLY 4.4 10.8 - - - +
40E VAL* 3.7 24.5 - - + +
99E ILE* 5.7 3.4 - - + -
100E ILE 3.8 5.8 - - - +
101E ALA* 3.4 26.9 - - + -
102E GLN 5.4 0.4 - - - +
106E MSE 5.9 8.1 - - + -
141E THR* 4.2 1.8 - - - -
146E GLY* 1.3 79.5 - - - +
148E ALA* 1.3 63.1 + - - +
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Residues in contact with ALA 148 (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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8E PHE* 4.3 12.3 - - + -
9E ASP 3.2 12.3 - - - +
10E VAL* 3.7 15.5 - - + -
40E VAL* 4.1 5.4 - - - +
99E ILE* 3.8 2.8 - - - +
100E ILE* 2.8 40.9 + - + +
140E PHE* 4.6 3.4 - - + -
141E THR* 4.0 15.9 - - + +
147E ILE* 1.3 75.4 - - - +
149E CYS* 1.3 65.0 + - - +
169E ACY 4.9 2.5 - - + -
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Residues in contact with CYS 149 (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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8E PHE* 3.3 10.0 - - - -
9E ASP 2.9 31.9 + - - +
40E VAL* 3.5 28.9 - - + +
41E ALA* 3.6 15.3 - - - -
44E ALA* 3.5 7.3 - - - +
97E ILE* 3.3 34.5 - - - -
98E THR 3.3 12.6 - - - -
99E ILE* 4.1 5.2 - - - -
100E ILE* 4.4 2.0 - - - +
148E ALA* 1.3 78.9 - - - +
150E GLU* 1.3 65.7 + - - +
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Residues in contact with GLU 150 (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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6D HIS* 3.2 29.9 + - + +
8D PHE* 4.6 4.0 - - - -
150D GLU* 2.6 32.1 - - - +
6E HIS* 2.8 24.3 + - + +
7E GLY 3.4 2.9 - - - +
8E PHE* 4.5 12.6 - - + +
96E ASP 4.1 0.2 - - - +
97E ILE* 3.6 0.3 - - - -
98E THR* 2.7 45.4 + - - +
100E ILE* 4.3 16.6 - - + +
149E CYS* 1.3 76.4 - - - +
151E ALA* 1.3 64.4 + - - +
150F GLU* 2.7 18.6 - - - +
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Residues in contact with ALA 151 (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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6D HIS* 5.6 0.7 - - - -
6E HIS* 3.2 7.2 - - - -
7E GLY 2.8 32.5 + - - +
44E ALA* 3.8 32.3 - - + +
45E LEU* 3.9 12.3 - - + +
48E ALA* 4.1 3.1 - - + -
96E ASP 3.5 9.6 - - - +
97E ILE* 4.2 11.7 - - + -
150E GLU* 1.3 77.7 - - - +
152E VAL* 1.3 67.1 + - - +
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Residues in contact with VAL 152 (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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4D ILE* 3.8 27.3 - - + +
5D GLY 4.2 3.1 - - - -
6D HIS* 3.7 41.1 - - + +
152D VAL* 4.7 9.9 - - + -
5E GLY 3.2 10.5 - - - +
6E HIS* 4.3 11.0 - - + -
45E LEU* 5.2 0.4 - - - +
48E ALA* 4.4 1.1 - - - -
94E ASN 4.4 0.2 - - - +
95E VAL* 3.5 4.9 - - - +
96E ASP* 3.2 41.3 + - + +
151E ALA* 1.3 81.2 - - - +
153E ALA* 1.3 60.7 + - - +
152F VAL* 4.9 4.9 - - + -
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Residues in contact with ALA 153 (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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4D ILE* 4.3 3.6 - - - -
3E ARG 3.7 0.5 - - - +
4E ILE* 3.5 5.7 - - - +
5E GLY 2.8 31.9 + - - -
45E LEU* 4.8 1.1 - - + -
48E ALA* 4.0 17.7 - - + +
49E ILE* 3.7 31.0 - - + -
52E ALA* 4.2 3.3 - - + +
92E ILE* 5.8 0.2 - - + -
94E ASN 3.8 4.5 - - - -
95E VAL* 3.9 11.0 - - + -
152E VAL* 1.3 74.8 - - - +
154E LEU* 1.3 61.9 + - - +
155E LEU* 4.1 2.9 - - + -
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Residues in contact with LEU 154 (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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2D ILE* 3.9 37.5 - - + +
3D ARG 4.4 0.9 - - - -
4D ILE* 3.6 23.8 - - + +
154D LEU* 4.6 5.4 - - + -
2E ILE* 3.4 24.5 - - + -
3E ARG 2.9 27.8 - - - +
4E ILE* 4.2 9.4 - - + -
92E ILE* 3.8 1.4 - - - +
93E GLY* 2.7 36.0 + - - -
94E ASN* 3.1 32.5 + - - +
153E ALA* 1.3 74.1 - - - +
155E LEU* 1.3 58.6 + - - +
156E ILE* 5.2 2.0 - - + -
154F LEU* 5.1 2.5 - - + -
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Residues in contact with LEU 155 (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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2E ILE* 3.5 6.4 - - - +
3E ARG* 2.8 33.8 + - + +
49E ILE* 3.9 26.9 - - + +
52E ALA* 3.9 19.5 - - + -
53E ALA* 3.9 11.9 - - + +
85E VAL* 3.4 33.4 - - + -
90E TYR* 3.9 18.2 - - + -
91E LYS 3.6 7.9 - - - +
92E ILE* 3.8 28.9 - - + -
153E ALA* 5.3 0.7 - - + -
154E LEU* 1.3 75.3 - - - +
156E ILE* 1.3 70.8 + - - +
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Residues in contact with ILE 156 (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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2D ILE* 4.8 18.2 - - + +
1E LEU 3.5 14.4 - - - +
2E ILE* 4.9 7.6 - - + -
90E TYR* 3.2 6.8 - - - -
91E LYS* 2.6 55.6 + - + +
92E ILE 5.0 0.4 - - - +
93E GLY* 3.8 23.6 - - - -
154E LEU* 4.8 4.5 - - + +
155E LEU* 1.3 80.9 - - - +
157E ARG* 1.3 74.9 + - + +
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Residues in contact with ARG 157 (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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0E SER 3.0 40.6 + - - +
1E LEU* 3.5 21.5 + - + +
88E LYS 4.0 12.6 + - - -
89E GLY* 3.0 20.1 + - - +
90E TYR* 3.5 20.4 + - - -
91E LYS* 3.9 7.1 - - - -
156E ILE* 1.3 89.8 - - + +
158E GLN* 1.3 71.2 + - - +
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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