Contacts of the strand formed by residues 146 - 157 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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138D LEU* 4.0 7.6 - - - +
11F HIS 3.2 14.1 - - - -
13F PHE* 3.6 14.1 - - - -
101F ALA* 5.3 0.3 - - - -
102F GLN 5.5 0.3 + - - -
140F PHE* 3.7 4.2 + - - -
141F THR* 3.4 26.4 - - - +
144F GLN* 3.2 2.8 - - - -
145F GLU* 1.3 83.7 + - - +
147F ILE* 1.3 68.9 + - - +
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Residues in contact with ILE 147 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10F VAL* 3.5 4.4 - - - +
11F HIS* 2.9 40.4 + - + +
13F PHE* 3.7 24.7 - - + -
38F GLY 4.8 5.4 - - - +
40F VAL* 3.8 28.6 - - + +
99F ILE* 5.8 2.9 - - + -
100F ILE 3.7 7.4 - - - +
101F ALA* 3.4 25.6 - - + -
102F GLN 5.2 1.1 - - - +
106F MSE 5.9 7.0 - - + -
140F PHE* 4.8 0.2 - - - -
141F THR* 4.0 4.3 - - - -
146F GLY* 1.3 79.9 - - - +
148F ALA* 1.3 64.0 + - - +
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Residues in contact with ALA 148 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8F PHE* 4.3 11.7 - - + -
9F ASP 3.4 13.0 - - - +
10F VAL* 4.0 12.8 - - + -
40F VAL* 4.1 4.8 - - - +
99F ILE* 3.6 6.1 - - - +
100F ILE* 2.6 48.0 + - + +
140F PHE* 4.5 3.4 - - + -
141F THR* 4.1 14.8 - - + -
147F ILE* 1.3 77.5 - - - +
149F CYS* 1.3 61.2 + - - +
170F ACY 4.9 2.0 - - + -
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Residues in contact with CYS 149 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8F PHE* 3.4 10.4 - - - -
9F ASP 3.1 28.5 + - - -
40F VAL* 3.6 27.4 - - + +
41F ALA* 3.7 16.2 - - - -
44F ALA* 3.7 8.6 - - - +
97F ILE* 3.7 22.9 - - - -
98F THR 3.2 15.0 - - - +
99F ILE* 4.2 5.2 - - - -
100F ILE* 4.4 1.8 - - - +
148F ALA* 1.3 80.1 - - - +
150F GLU* 1.3 72.6 + - - +
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Residues in contact with GLU 150 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150D GLU* 3.1 10.3 - - - +
6E HIS* 3.2 36.8 - - + +
8E PHE* 5.5 2.1 - - + -
150E GLU* 2.7 20.1 - - - +
6F HIS* 2.5 36.4 + - + +
7F GLY 3.3 8.2 - - - +
8F PHE* 3.5 19.8 - - + +
98F THR* 2.8 39.6 + - - +
100F ILE* 4.9 11.3 - - + +
149F CYS* 1.3 77.1 - - - +
151F ALA* 1.3 64.3 + - - +
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Residues in contact with ALA 151 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6E HIS* 5.8 1.3 - - - -
6F HIS* 3.4 5.5 - - - -
7F GLY 2.8 33.7 + - - +
44F ALA* 3.9 9.9 - - + +
45F LEU* 3.8 24.0 - - - +
48F ALA* 4.1 1.8 - - + -
96F ASP 3.6 4.7 - - - -
97F ILE* 3.4 27.1 - - + -
150F GLU* 1.3 78.6 - - - +
152F VAL* 1.3 67.2 + - - +
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Residues in contact with VAL 152 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152D VAL* 5.0 4.9 - - + -
4E ILE* 4.1 23.0 - - + +
5E GLY 4.1 5.2 - - - +
6E HIS* 3.6 43.3 - - + +
152E VAL* 4.9 9.0 - - + -
4F ILE* 6.2 0.2 - - + -
5F GLY 3.2 11.0 - - - +
6F HIS* 4.5 10.3 - - + -
48F ALA* 4.2 1.8 - - - -
95F VAL* 3.9 2.9 - - - +
96F ASP* 3.1 42.6 + - + +
97F ILE* 4.5 1.7 - - - +
151F ALA* 1.3 80.5 - - - +
153F ALA* 1.3 62.4 + - - +
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Residues in contact with ALA 153 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4E ILE* 4.2 4.3 - - - -
3F ARG 3.6 0.3 - - - +
4F ILE* 3.4 6.6 - - - +
5F GLY 2.8 36.1 + - - -
45F LEU* 4.9 0.7 - - + -
48F ALA* 4.0 15.5 - - + +
49F ILE* 3.9 25.1 - - + +
52F ALA* 4.4 1.9 - - + +
92F ILE* 6.5 0.2 - - + -
94F ASN 3.9 4.5 - - - -
95F VAL* 3.9 17.3 - - + -
152F VAL* 1.3 76.9 - - - +
154F LEU* 1.3 61.5 + - - +
155F LEU* 5.1 3.1 - - + -
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Residues in contact with LEU 154 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154D LEU* 5.2 2.0 - - + -
2E ILE* 3.7 39.5 - - + +
3E ARG 4.5 1.1 - - - +
4E ILE* 3.7 15.7 - - + +
154E LEU* 5.1 2.2 - - + -
2F ILE* 3.2 29.6 - - + -
3F ARG 3.0 19.5 - - - +
4F ILE* 4.3 6.7 - - + +
92F ILE* 4.1 0.9 - - - +
93F GLY* 2.7 35.8 + - - -
94F ASN* 3.1 34.6 + - - +
95F VAL* 5.8 0.2 - - - +
153F ALA* 1.3 74.9 - - - +
155F LEU* 1.3 64.8 + - - +
156F ILE* 4.8 5.2 - - + -
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Residues in contact with LEU 155 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1F LEU 3.6 0.5 - - - +
2F ILE* 3.3 6.9 - - - -
3F ARG* 2.7 42.7 + - + -
49F ILE* 3.9 20.2 - - + +
52F ALA* 3.8 22.2 - - + -
53F ALA* 3.8 25.4 - - + +
85F VAL* 3.6 31.6 - - + -
90F TYR* 3.8 13.6 - - + -
91F LYS 3.4 9.6 - - - +
92F ILE* 4.2 16.6 - - + -
153F ALA* 5.1 1.1 - - + -
154F LEU* 1.3 83.0 - - - +
156F ILE* 1.3 63.9 + - - +
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Residues in contact with ILE 156 (chain F).
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* 5.4 8.5 - - - +
2E ILE* 5.6 5.6 - - + +
1F LEU* 3.3 10.3 - - + +
2F ILE* 4.8 14.6 - - + -
90F TYR* 4.0 2.0 - - - -
91F LYS* 2.7 62.4 + - - +
92F ILE 4.8 0.9 - - - +
93F GLY* 3.4 28.3 - - - -
154F LEU* 4.8 7.0 - - + -
155F LEU* 1.3 78.9 - - - +
157F ARG* 1.3 73.3 + - - +
158F GLN 3.2 0.7 + - - -
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Residues in contact with ARG 157 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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0F SER 3.7 15.7 + - - +
1F LEU* 2.9 42.6 + - + +
88F LYS 3.4 25.0 + - - -
89F GLY* 3.3 14.4 + - - +
90F TYR* 3.8 26.4 + - + -
91F LYS* 5.3 0.7 + - - -
156F ILE* 1.3 78.9 - - - +
158F GLN* 1.3 70.4 + - - +
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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