Contacts of the strand formed by residues 23 - 30 (chain B) in PDB entry 3V98
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 TYR 23 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22B ASP* 1.3 71.1 - - - +
24B ILE* 1.3 61.3 + - - +
25B TYR* 3.7 26.5 - - + -
39B LEU* 3.7 26.2 - - + -
41B ASP 4.4 7.4 - - - -
42B LYS* 4.6 15.9 - - + -
70B GLU 3.7 0.7 - - - +
71B LYS* 3.4 5.4 - - - -
72B ARG* 3.0 47.8 + - + +
73B LYS 3.8 9.2 - - - -
74B TYR* 3.5 47.9 - + + -
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Residues in contact with ILE 24 (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 THR* 4.4 3.1 - - + -
22B ASP 3.6 5.5 + - - +
23B TYR* 1.3 79.9 - - - +
25B TYR* 1.3 69.9 + - - +
39B LEU* 3.4 6.1 - - - +
40B LEU* 2.9 45.4 + - + +
41B ASP 4.3 3.3 + - - -
45B PHE* 3.3 36.6 - - + -
69B ILE* 4.2 8.5 - - + -
70B GLU 3.6 1.6 - - - +
71B LYS* 3.9 25.8 - - + -
80B TRP* 3.6 44.0 - - + -
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Residues in contact with TYR 25 (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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23B TYR* 3.7 28.2 - - + +
24B ILE* 1.3 75.0 - - - +
26B LEU* 1.3 61.9 + - - +
27B SER* 5.6 0.2 - - - -
37B LYS* 3.8 29.8 - - + -
38B HIS 3.3 4.7 - - - -
39B LEU* 3.5 45.1 - - + +
68B ARG 3.9 0.2 - - - +
69B ILE* 3.5 7.8 - - - +
70B GLU* 2.8 46.6 + - + +
72B ARG* 3.2 51.0 + - + +
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Residues in contact with LEU 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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8B VAL* 3.6 35.4 - - + -
10B VAL* 4.9 0.7 - - + -
25B TYR* 1.3 76.6 - - - +
27B SER* 1.3 67.3 + - - +
28B LEU* 3.6 30.1 - - + -
36B GLU 3.7 1.6 - - - +
37B LYS* 4.6 0.9 - - - -
38B HIS* 2.8 40.0 + - + +
40B LEU* 4.2 28.3 - - + -
55B VAL* 5.6 6.3 - - + -
67B VAL* 4.1 10.5 - - + -
68B ARG 3.3 4.3 - - - +
69B ILE* 3.5 24.7 - - + -
85B ILE* 4.3 4.7 - - + -
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Residues in contact with SER 27 (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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26B LEU* 1.3 79.0 - - - +
28B LEU* 1.3 68.4 + - - +
34B CYS* 5.8 1.3 - - - -
35B SER* 3.6 13.0 - - - -
36B GLU 3.9 11.4 - - - -
37B LYS* 4.3 16.4 - - - +
67B VAL* 3.7 2.8 - - - -
68B ARG* 2.8 61.8 + - - +
108B GLU* 4.8 1.2 + - - -
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Residues in contact with LEU 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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6B TYR* 3.8 50.3 - - + -
8B VAL* 5.1 1.6 - - + -
26B LEU* 3.6 24.9 - - + -
27B SER* 1.3 74.3 - - - +
29B VAL* 1.3 62.9 + - - +
30B GLY 3.8 1.1 + - - -
34B CYS* 3.3 4.7 - - - +
35B SER* 2.8 44.5 + - - +
55B VAL* 5.2 8.7 - - + -
61B LEU* 4.0 12.7 - - + +
64B ILE* 4.1 9.0 - - + -
66B LEU 3.9 2.0 - - - +
67B VAL* 4.0 12.1 - - + -
87B LEU* 4.0 26.0 - - + -
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Residues in contact with VAL 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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27B SER* 5.8 0.2 - - - -
28B LEU* 1.3 74.7 - - - +
30B GLY* 1.3 61.6 + - - +
34B CYS* 3.9 17.9 - - + -
64B ILE* 3.7 2.8 - - - -
65B GLN* 2.7 31.9 + - - +
66B LEU* 2.9 31.9 + - + +
68B ARG* 3.1 50.9 - - + +
126B ILE* 4.1 27.4 - - + -
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Residues in contact with GLY 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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28B LEU 3.8 2.0 + - - -
29B VAL* 1.3 76.5 - - - +
31B SER* 1.3 64.8 + - - +
32B ALA 3.3 2.2 - - - -
33B GLY* 2.9 27.0 + - - +
34B CYS* 5.6 0.2 - - - -
61B LEU* 3.4 14.6 - - - +
63B GLU 3.2 15.3 - - - -
64B ILE* 4.2 2.4 - - - +
65B GLN* 4.3 4.0 - - - -
126B ILE* 3.7 12.1 - - - +
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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