Contacts of the strand formed by residues 38 - 45 (chain B) in PDB entry 2JWN
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 38 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34B ILE 2.9 14.6 + - - -
35B ASP* 2.8 15.3 + - - +
37B ARG* 1.3 79.9 - - - +
39B VAL* 1.3 66.1 + - - +
82B TYR* 4.2 0.7 - - - +
83B ILE 3.1 7.0 + - - -
84B GLU* 3.2 19.0 - - - +
91B VAL* 3.3 7.3 - - - +
111B PRO* 3.2 8.7 - - - +
112B LYS* 2.9 47.8 + - - +
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Residues in contact with VAL 39 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B SER* 1.3 82.8 + - - +
40B TYR* 1.3 79.4 + - - +
41B VAL* 4.6 2.5 - - + -
57B PHE* 4.9 0.9 - - + -
82B TYR* 3.1 7.1 - - - +
83B ILE* 2.7 34.3 + - + +
85B PHE* 3.5 31.4 - - + -
91B VAL* 3.6 17.0 - - + +
94B ALA* 3.9 13.0 - - + -
95B VAL* 4.1 6.5 - - + -
109B VAL* 3.7 16.4 - - + -
110B LEU 3.3 23.1 - - - +
112B LYS* 3.8 4.3 - - - -
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Residues in contact with TYR 40 (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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20A GLU* 3.1 21.9 - - + +
21A GLY* 3.0 46.3 + - - -
22A PRO* 3.7 2.5 - - + -
39B VAL* 1.3 73.2 - - - +
41B VAL* 1.3 60.5 + - - +
42B GLY* 3.4 28.7 - - - -
43B ASN 4.5 0.5 + - - -
80B TYR* 3.5 28.8 - + + -
81B ALA 3.6 2.7 - - - -
82B TYR* 3.4 26.9 - + + -
108B LYS* 3.2 9.9 - - + +
109B VAL* 2.9 28.9 - - - +
110B LEU* 2.6 44.2 + - + +
111B PRO 4.9 0.2 - - - -
112B LYS* 4.3 7.6 - - + -
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Residues in contact with VAL 41 (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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39B VAL* 4.6 2.7 - - + -
40B TYR* 1.3 79.6 - - - +
42B GLY* 1.3 59.4 + - - +
44B VAL* 4.2 16.6 - - + +
53B LEU* 4.4 9.6 - - + -
57B PHE* 3.3 35.7 - - + -
80B TYR* 3.3 1.7 - - - +
81B ALA* 2.6 45.2 + - + +
83B ILE* 3.4 26.9 - - + -
107B ILE* 4.4 12.8 - - + -
108B LYS 3.4 3.1 - - - -
109B VAL* 3.8 13.9 - - + -
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Residues in contact with GLY 42 (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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20A GLU* 5.6 1.6 - - - -
40B TYR* 3.4 27.4 - - - -
41B VAL* 1.3 75.4 - - - +
43B ASN* 1.3 65.6 + - - +
44B VAL* 3.0 12.2 + - - -
79B GLY 4.1 3.6 - - - -
80B TYR* 4.2 0.2 - - - -
107B ILE* 3.3 19.1 - - - +
108B LYS* 2.8 17.9 + - - -
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Residues in contact with ASN 43 (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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13A MET 4.1 1.7 - - - +
14A THR* 2.8 44.9 + - + +
20A GLU* 5.6 6.5 - - + +
40B TYR* 4.5 2.4 + - - -
42B GLY* 1.3 71.4 - - - +
44B VAL* 1.3 62.1 + - - +
78B LYS* 6.4 1.3 - - - +
79B GLY 3.2 9.4 + - - +
80B TYR* 5.0 3.0 - - - -
105B ARG* 2.7 68.1 + - - +
106B THR 2.7 30.4 + - - +
107B ILE* 4.1 4.3 - - - +
108B LYS* 4.8 2.5 - - + +
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Residues in contact with VAL 44 (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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41B VAL* 4.2 24.2 - - + +
42B GLY 3.0 5.0 + - - +
43B ASN* 1.3 75.8 - - - +
45B ASP* 1.3 66.9 + - - +
48B SER* 3.5 30.5 - - - +
53B LEU* 4.4 17.0 - - + -
68B ILE* 5.2 3.8 - - + -
79B GLY* 3.0 50.6 + - - +
80B TYR* 3.9 6.7 - - - +
81B ALA* 4.3 9.0 - - + +
102B PHE* 4.7 11.7 - - + -
105B ARG* 4.9 0.7 - - - +
107B ILE* 4.2 9.0 - - + -
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Residues in contact with ASP 45 (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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9A THR* 4.8 6.2 + - - -
11A SER* 3.6 14.0 + - - -
43B ASN 3.3 2.9 + - - -
44B VAL* 1.3 81.5 - - - +
46B TYR* 1.3 57.9 + - - +
47B GLY* 2.7 36.5 + - - -
48B SER* 2.9 21.5 + - - +
78B LYS* 5.5 0.4 - - - +
79B GLY* 4.8 2.6 - - - +
102B PHE* 5.6 0.9 - - - -
103B ARG* 3.1 30.0 - - - +
105B ARG* 3.3 44.9 - - - +
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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