Contacts of the strand formed by residues 146 - 157 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11D HIS 3.3 14.6 - - - -
13D PHE* 3.5 13.6 - - - -
101D ALA* 5.4 0.3 - - - -
102D GLN 5.5 0.2 + - - -
140D PHE* 3.6 4.6 + - - -
141D THR* 3.4 25.9 - - - +
144D GLN* 3.2 3.0 - - - -
145D GLU* 1.3 82.1 + - - +
147D ILE* 1.3 69.2 + - - +
138E LEU* 3.9 7.6 - - - +
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Residues in contact with ILE 147 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10D VAL* 3.5 3.8 - - - +
11D HIS* 3.0 46.9 + - + +
13D PHE* 3.8 23.3 - - + -
38D GLY 4.8 5.6 - - - +
40D VAL* 4.0 22.5 - - + +
99D ILE* 5.7 3.8 - - + -
100D ILE 3.8 7.6 - - - +
101D ALA* 3.7 24.0 - - + -
102D GLN 5.2 1.6 - - - +
140D PHE* 4.9 0.4 - - - -
141D THR* 4.0 3.4 - - - -
146D GLY* 1.3 79.3 - - - +
148D ALA* 1.3 62.7 + - - +
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Residues in contact with ALA 148 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8D PHE* 4.1 14.1 - - + -
9D ASP 3.4 13.2 - - - +
10D VAL* 3.8 12.6 - - + -
40D VAL* 3.7 7.4 - - - +
99D ILE* 4.0 3.5 - - - +
100D ILE* 3.0 40.8 + - + +
140D PHE* 4.5 4.3 - - + -
141D THR* 3.8 11.3 - - + +
147D ILE* 1.3 76.6 - - - +
149D CYS* 1.3 68.0 + - - +
171D ACY 5.0 1.8 - - + -
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Residues in contact with CYS 149 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8D PHE* 3.4 9.3 - - - -
9D ASP 3.2 26.8 + - - -
40D VAL* 3.4 26.5 - - + +
41D ALA* 3.5 17.7 - - - -
44D ALA* 3.6 8.3 - - - +
97D ILE* 3.4 34.1 - - - -
98D THR 3.3 13.5 - - - -
99D ILE* 4.2 5.8 - - - -
100D ILE* 4.3 2.0 - - - +
148D ALA* 1.3 82.1 - - - +
150D GLU* 1.3 63.0 + - - +
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Residues in contact with GLU 150 (chain D).
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* 2.7 18.0 + - + +
7D GLY 3.5 2.7 - - - +
8D PHE* 4.2 14.1 - - + -
96D ASP 4.3 0.2 - - - +
97D ILE* 3.6 1.4 - - - +
98D THR* 2.7 41.3 + - - +
100D ILE* 4.7 12.7 - - + +
149D CYS* 1.3 75.6 - - - +
151D ALA* 1.3 64.9 + - - +
6E HIS* 4.5 0.3 + - - -
150E GLU* 2.6 39.9 - - - +
6F HIS* 3.2 38.5 + - + +
8F PHE* 5.1 0.9 - - - -
150F GLU* 3.1 16.2 - - - +
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Residues in contact with ALA 151 (chain D).
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 5.5 - - - -
7D GLY 2.7 37.2 + - - +
44D ALA* 3.8 31.9 - - + +
45D LEU* 3.9 9.4 - - + +
48D ALA* 4.1 2.7 - - + -
96D ASP 3.5 9.4 - - - +
97D ILE* 4.0 15.9 - - + -
150D GLU* 1.3 78.3 - - - +
152D VAL* 1.3 66.7 + - - +
6F HIS* 5.6 0.4 - - - -
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Residues in contact with VAL 152 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5D GLY 3.0 12.3 - - - +
6D HIS* 4.4 13.5 - - + -
45D LEU* 5.1 0.6 - - - +
48D ALA* 4.3 2.0 - - - -
94D ASN 4.4 0.2 - - - +
95D VAL* 3.5 3.5 - - - +
96D ASP* 3.0 44.4 + - + +
151D ALA* 1.3 82.7 - - - +
153D ALA* 1.3 61.3 + - - +
152E VAL* 4.7 9.2 - - + -
4F ILE* 3.9 25.5 - - + +
5F GLY 4.2 1.8 - - - -
6F HIS* 3.5 43.3 - - + +
152F VAL* 5.0 5.4 - - + -
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Residues in contact with ALA 153 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3D ARG 3.7 0.3 - - - +
4D ILE* 3.5 3.3 - - - -
5D GLY* 2.8 31.7 + - - +
45D LEU* 4.8 0.4 - - + -
48D ALA* 4.0 27.1 - - + +
49D ILE* 4.3 11.0 - - + +
52D ALA* 4.5 1.9 - - + +
94D ASN 3.7 5.4 - - - -
95D VAL* 3.7 18.8 - - + -
152D VAL* 1.3 74.9 - - - +
154D LEU* 1.3 62.4 + - - +
155D LEU* 4.1 6.1 - - + -
4F ILE* 4.1 6.3 - - - +
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Residues in contact with LEU 154 (chain D).
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* 3.6 26.2 - - + -
3D ARG 3.3 15.5 - - - +
4D ILE* 4.2 11.9 - - + +
92D ILE* 4.1 2.4 - - - +
93D GLY* 2.6 35.4 + - - -
94D ASN* 3.0 28.2 + - - +
153D ALA* 1.3 75.1 - - - +
155D LEU* 1.3 56.6 - - - +
156D ILE* 4.9 7.6 - - + -
154E LEU* 4.6 5.6 - - + -
2F ILE* 3.4 44.6 - - + +
4F ILE* 3.7 18.6 - - + +
154F LEU* 5.7 1.6 - - + -
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Residues in contact with LEU 155 (chain D).
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* 3.3 6.8 - - - +
3D ARG* 2.6 46.7 + - + +
49D ILE* 3.8 13.0 - - + +
52D ALA* 3.6 29.4 - - + -
53D ALA* 3.6 19.7 - - + +
85D VAL* 3.6 28.3 - - + -
90D TYR* 4.1 13.5 - - + -
91D LYS 3.5 6.7 - - - +
92D ILE* 3.7 31.2 - - + -
153D ALA* 5.1 3.8 - - + -
154D LEU* 1.3 76.9 - - - +
156D ILE* 1.3 63.5 + - - +
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Residues in contact with ILE 156 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1D LEU 3.5 9.2 - - - +
2D ILE* 4.5 12.1 - - + -
90D TYR* 3.6 4.4 - - - -
91D LYS* 2.7 75.4 + - - +
92D ILE 3.7 15.3 - - - +
93D GLY* 3.9 14.6 - - - -
127D GLN* 5.5 1.8 - - - +
154D LEU* 4.9 5.6 - - + +
155D LEU* 1.3 80.5 - - - +
157D ARG* 1.3 64.1 + - - +
0F SER* 4.8 18.2 - - - +
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Residues in contact with ARG 157 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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0D SER 2.9 61.1 + - - +
1D LEU* 3.1 31.0 + - + +
88D LYS* 3.2 22.2 + - - +
89D GLY* 3.2 24.1 + - - -
90D TYR* 4.1 14.5 + - + -
91D LYS* 4.6 4.3 + - - -
156D ILE* 1.3 76.9 - - - +
158D GLN* 1.3 66.9 + - - +
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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