Contacts of the strand formed by residues 25 - 34 (chain B) in PDB entry 2VJD
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 SER 25 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21B PRO* 3.4 2.4 - - - +
22B VAL 2.7 31.0 + - - -
23B LEU 4.1 0.4 - - - -
24B SER* 1.3 75.1 - - - +
26B HIS* 1.3 87.8 + - - -
103B SER 5.6 1.0 + - - -
137B TYR* 3.3 40.7 + - - -
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Residues in contact with HIS 26 (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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19B ARG* 4.0 31.6 - - + -
20B VAL 3.3 8.5 - - - +
21B PRO* 3.7 25.0 - - + +
22B VAL* 3.9 1.7 - - - +
24B SER 4.8 5.4 - - - -
25B SER* 1.3 110.4 + - - +
27B ILE* 1.3 72.4 + - - +
103B SER* 4.0 16.6 - - - +
137B TYR* 4.5 1.2 - - - -
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Residues in contact with ILE 27 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B ARG* 3.7 5.7 - - - +
20B VAL* 2.8 46.7 + - + +
22B VAL* 3.8 5.6 - - + -
26B HIS* 1.3 81.4 - - - +
28B SER* 1.3 61.4 + - - +
100B TRP* 3.6 21.1 - - + -
101B VAL 3.6 12.6 - - - +
102B PRO* 4.5 9.4 - - + -
103B SER* 4.0 9.0 - - - +
133B LYS* 3.3 43.5 - - + +
136B ALA* 4.9 4.0 - - + -
137B TYR* 3.7 32.1 - - + -
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Residues in contact with SER 28 (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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5B GLU* 4.1 17.3 + - - +
6B LEU* 3.9 19.0 - - - +
18B THR 3.7 4.9 - - - -
19B ARG* 4.8 3.0 + - - +
27B ILE* 1.3 78.2 - - - +
29B ALA* 1.3 61.1 + - - +
30B PHE* 3.8 22.4 - - - -
100B TRP* 3.5 3.8 - - - -
101B VAL* 2.9 43.2 + - - +
102B PRO 4.9 0.7 + - - -
103B SER* 4.3 10.1 - - - -
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Residues in contact with ALA 29 (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 GLY* 3.2 3.1 - - - -
18B THR* 2.9 39.4 + - + +
20B VAL* 3.7 27.6 - - + -
28B SER* 1.3 76.4 - - - +
30B PHE* 1.3 64.0 + - - +
31B LEU* 3.9 12.1 - - + -
99B ILE 3.3 4.9 - - - +
100B TRP* 4.0 22.2 - - + +
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Residues in contact with PHE 30 (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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5B GLU 3.6 21.8 - - - -
6B LEU* 3.4 25.6 - - - -
8B VAL* 3.9 14.8 - - + -
15B VAL* 3.9 12.1 - - + -
17B GLY* 3.7 15.3 - - - -
28B SER* 3.8 23.3 - - - -
29B ALA* 1.3 74.3 - - - +
31B LEU* 1.3 61.4 + - - +
33B ILE* 3.6 19.7 - - + +
60B ALA* 3.6 6.7 - - + -
97B LEU 4.0 1.7 - - - +
98B ASN* 3.3 4.5 - - - -
99B ILE* 2.8 46.8 + - + +
101B VAL* 4.1 13.7 - - + -
105B ARG* 5.1 0.7 - - - -
187B PHE* 3.6 32.8 - + - -
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Residues in contact with LEU 31 (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 THR* 4.8 3.1 - - + -
20B VAL* 5.7 3.1 - - + -
29B ALA* 4.2 21.3 - - + +
30B PHE* 1.3 80.8 - - - +
32B GLY* 1.3 64.1 + - - +
33B ILE 3.6 0.2 - - - -
59B ASN 4.5 0.7 - - - +
60B ALA* 2.8 35.7 + - - +
61B SER* 3.8 20.6 - - - +
62B THR* 3.4 20.4 - - - +
63B TYR* 4.0 26.0 - - + +
98B ASN* 3.6 13.2 - - + +
99B ILE 4.7 0.4 - - - +
100B TRP* 3.9 29.2 - - + +
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Residues in contact with GLY 32 (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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31B LEU* 1.3 73.1 - - - +
33B ILE* 1.3 61.2 + - - +
58B TRP* 3.4 19.7 + - - -
62B THR 4.2 2.5 - - - -
64B PRO* 3.7 31.1 - - - +
96B TYR* 3.3 17.6 - - - -
97B LEU 3.4 2.8 + - - -
98B ASN* 2.9 14.7 + - - -
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Residues in contact with ILE 33 (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 VAL* 3.8 27.6 - - + -
30B PHE* 3.6 31.4 - - + +
32B GLY* 1.3 72.2 - - - -
34B PRO* 1.3 79.0 - - + +
54B TRP* 4.8 3.6 - - + -
58B TRP* 4.8 1.3 - - + +
60B ALA* 4.1 16.4 - - + -
96B TYR* 3.2 1.5 - - - -
97B LEU* 2.7 50.8 + - + +
99B ILE* 4.3 11.4 - - + -
179B TRP* 3.9 22.4 - - + +
187B PHE* 4.3 16.8 - - + -
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Residues in contact with PRO 34 (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 SER* 6.0 0.3 - - - -
32B GLY 3.6 8.3 - - - +
33B ILE* 1.3 97.0 - - + +
35B PHE* 1.3 60.0 + - - +
36B ALA 4.4 3.8 - - - +
51B LYS* 4.0 28.8 - - + +
54B TRP* 4.1 12.1 - - + -
58B TRP* 3.6 40.6 - - + -
95B LEU 3.7 4.7 - - - +
96B TYR* 3.5 23.7 - - + -
179B TRP* 4.2 6.8 + - - -
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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