Contacts of the strand formed by residues 12 - 22 (chain B) in PDB entry 3VHT
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 12 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7B LEU 3.5 25.1 - - - +
8B PHE* 4.4 6.3 - - + -
9B THR 4.8 0.4 - - - +
10B GLY 4.0 9.2 - - - +
11B VAL* 1.3 76.9 - - - +
13B PRO* 1.3 85.8 - - + +
14B ILE* 3.6 1.2 - - - +
34B GLU* 3.2 3.7 - - - -
35B GLY 2.8 31.6 + - - -
71B PHE* 3.8 20.2 - - + -
114B PHE* 3.8 19.3 - - + -
117B ASP 3.7 11.7 - - - +
119B LEU* 3.8 12.6 - - + -
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Residues in contact with PRO 13 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11B VAL* 3.9 7.7 - - + +
12B VAL* 1.3 88.5 - - - +
14B ILE* 1.3 59.7 + - - +
33B GLY 3.6 8.7 - - - +
34B GLU* 4.2 4.2 - - + -
117B ASP* 3.5 41.1 - - + +
118B THR* 3.5 15.9 - - + -
119B LEU 3.0 24.1 + - - -
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Residues in contact with ILE 14 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12B VAL 3.6 6.3 - - - +
13B PRO* 1.3 81.6 - - - +
15B LEU* 1.3 70.3 + - - +
16B VAL* 4.3 6.7 - - + -
32B GLU* 3.3 6.1 - - - +
33B GLY 2.7 34.8 + - - +
34B GLU 3.3 3.1 - - - +
35B GLY 3.3 18.2 - - - +
42B LEU* 3.3 33.0 - - + -
44B LEU* 3.9 18.2 - - + -
68B VAL* 4.6 7.6 - - + -
71B PHE* 3.4 27.4 - - + -
118B THR* 4.7 1.3 - - - -
119B LEU* 3.2 20.2 - - + +
120B VAL* 5.4 0.2 - - - -
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Residues in contact with LEU 15 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14B ILE* 1.3 76.7 - - - +
16B VAL* 1.3 68.8 + - - +
17B GLU* 3.6 31.8 - - + +
30B SER* 5.8 1.3 - - - -
31B GLY 3.5 16.6 - - - +
32B GLU* 4.9 6.1 - - + -
118B THR* 4.1 19.0 + - + +
119B LEU 3.0 6.5 + - - +
120B VAL* 3.2 14.9 - - + +
121B ASN* 2.8 26.5 + - - +
122B ARG* 6.3 1.1 - - - +
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Residues in contact with VAL 16 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14B ILE* 4.3 15.0 - - + -
15B LEU* 1.3 76.5 - - - +
17B GLU* 1.3 76.6 + - - +
29B VAL 5.6 0.4 - - - +
30B SER* 3.4 0.9 - - - -
31B GLY* 2.8 34.4 + - - +
44B LEU* 4.4 9.4 - - + -
46B PHE* 3.9 21.5 - - + -
64B PHE* 3.7 43.3 - - + +
68B VAL* 5.7 0.4 - - + -
121B ASN* 3.4 17.7 - - + +
123B ILE* 3.8 12.6 - - + -
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Residues in contact with GLU 17 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15B LEU* 3.6 22.4 - - + +
16B VAL* 1.3 82.1 - - - +
18B LEU* 1.3 56.2 + - - +
29B VAL 3.6 3.1 - - - +
30B SER* 2.5 29.2 + - - -
120B VAL* 6.6 0.2 - - + -
121B ASN 2.9 11.2 + - - +
122B ARG* 3.3 30.1 + - + +
123B ILE* 2.7 33.7 + - - +
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Residues in contact with LEU 18 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17B GLU* 1.3 77.0 - - - +
19B ASP* 1.3 69.0 + - - +
20B GLY* 3.5 15.3 - - - +
27B PHE* 3.5 33.7 - - + -
28B SER* 3.3 6.9 - - - -
29B VAL* 2.9 41.1 + - + +
60B LEU* 4.8 2.9 - - + -
63B THR* 3.6 31.6 - - + -
64B PHE* 3.9 27.1 - - + -
123B ILE* 3.3 19.3 - - + +
125B LEU* 4.2 13.5 - - + -
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Residues in contact with ASP 19 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18B LEU* 1.3 76.9 - - - +
20B GLY* 1.3 58.9 + - - +
27B PHE 3.7 3.8 - - - +
28B SER* 3.1 20.3 + - - -
123B ILE 3.1 9.1 + - - +
124B GLU* 3.5 13.5 - - + +
125B LEU 3.0 24.3 + - - +
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Residues in contact with GLY 20 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18B LEU* 3.5 14.4 - - - +
19B ASP* 1.3 75.0 - - - +
21B ASP* 1.3 61.0 + - - +
26B LYS* 3.5 8.7 + - - +
27B PHE* 2.9 47.3 + - - +
125B LEU* 3.4 9.2 - - - -
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Residues in contact with ASP 21 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20B GLY* 1.3 75.1 - - - +
22B VAL* 1.3 53.8 + - - +
23B ASN 4.2 0.3 + - - -
24B GLY* 3.2 31.0 + - - -
25B HIS 3.4 6.1 - - - -
26B LYS* 3.8 30.0 + - + +
27B PHE* 4.1 1.0 - - - -
125B LEU* 3.2 8.8 + - - +
126B LYS* 3.4 29.6 + - + +
127B GLY 2.6 32.1 + - - +
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Residues in contact with VAL 22 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21B ASP* 1.3 78.1 + - - +
23B ASN* 1.3 66.6 + - + +
24B GLY 3.1 0.2 - - - -
25B HIS* 2.8 40.6 + - + +
27B PHE* 4.0 14.6 - - + -
55B VAL* 3.9 24.9 - - + -
106B TYR* 3.8 11.2 - - + -
125B LEU* 3.4 25.6 - - + -
127B GLY* 3.3 8.1 - - - -
130B PHE* 3.7 30.5 - - + -
137B LEU* 4.4 6.3 - - + -
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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