Contacts of the strand formed by residues 35 - 42 (chain B) in PDB entry 5DPT
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 ARG 35 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5A ASN* 3.1 24.2 + - - +
6A VAL 4.3 2.0 + - - +
88A ASN* 3.3 47.5 + - - +
89A ASN* 5.3 0.2 - - + -
90A THR* 4.2 5.6 - - + -
104A ASP 4.9 0.2 + - - -
105A ASN* 3.2 25.7 + - - -
29B ARG* 2.9 20.3 + - - +
32B TYR* 3.2 45.9 + - + +
34B ASP* 1.3 85.2 - - - +
36B VAL* 1.3 65.3 + - - +
37B PRO* 3.6 5.1 - - - +
57B LEU* 3.0 52.9 + - + +
58B VAL 3.4 10.2 + - - +
59B PRO* 5.1 3.1 - - + +
60B SER 4.5 0.7 - - - +
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Residues in contact with VAL 36 (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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29B ARG* 4.5 4.3 - - - +
35B ARG* 1.3 76.3 - - - +
37B PRO* 1.3 63.7 - - - +
38B VAL* 3.5 19.9 + - + -
56B TYR 3.4 3.8 - - - +
57B LEU* 3.8 2.5 - - - -
58B VAL* 2.5 49.6 + - + +
60B SER* 3.9 16.4 - - - -
98B MET* 3.8 20.9 - - + +
99B GLY* 3.9 15.5 - - - -
102B TYR* 3.6 34.5 - - + -
112B LEU* 4.3 2.7 - - + -
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Residues in contact with PRO 37 (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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3A TRP* 3.6 23.8 - - + -
28B ILE* 4.1 14.1 - - + -
29B ARG* 4.6 7.0 - - + +
35B ARG 3.6 9.2 - - - +
36B VAL* 1.3 82.4 - - - +
38B VAL* 1.3 59.8 + - - +
56B TYR 3.3 6.5 - - - +
57B LEU* 3.7 12.8 - - + -
102B TYR* 3.8 16.9 - - + +
110B TYR 3.6 22.4 - - - +
111B PHE* 3.8 10.0 - - + -
112B LEU* 3.1 26.5 + - - +
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Residues in contact with VAL 38 (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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3A TRP* 4.0 0.8 - - - -
36B VAL* 3.6 26.9 - - + +
37B PRO* 1.3 77.5 - - - +
39B ILE* 1.3 67.0 + - - +
40B VAL* 3.8 16.2 - - + -
54B ARG 3.5 2.8 - - - +
55B LYS* 3.7 1.9 - - - -
56B TYR* 2.6 45.5 + - + +
58B VAL* 4.1 7.6 - - + -
67B PHE* 4.3 6.3 - - + -
98B MET* 3.7 18.6 - - + -
112B LEU* 3.2 15.5 - - + +
114B VAL* 3.7 26.5 - - + -
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Residues in contact with ILE 39 (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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3A TRP* 4.5 11.0 - - + -
12B TYR* 3.8 42.0 - - + -
38B VAL* 1.3 76.9 - - - +
40B VAL* 1.3 63.3 + - - +
41B GLU* 3.9 14.8 + - - +
54B ARG* 3.6 8.5 - - + +
55B LYS* 3.7 28.0 - - + -
111B PHE* 4.3 15.0 - - + -
112B LEU 2.7 9.5 + - - -
113B TYR* 3.5 37.0 - - + +
114B VAL 2.8 29.1 + - - +
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Residues in contact with VAL 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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38B VAL* 3.8 19.3 - - + -
39B ILE* 1.3 73.7 - - - +
41B GLU* 1.3 66.2 + - - +
51B LEU* 3.9 24.3 - - + +
54B ARG* 2.9 32.1 + - - +
56B TYR* 3.9 10.3 - - + -
67B PHE* 3.9 23.8 - - + -
71B ILE* 4.4 11.9 - - + -
85B PHE* 5.1 1.8 - - + -
114B VAL* 3.3 16.4 - - + +
116B TYR* 3.6 24.5 - - + -
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Residues in contact with GLU 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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11B GLN* 3.7 35.8 + - + +
12B TYR* 3.2 29.4 + - - +
13B LYS* 4.6 9.0 - - - +
39B ILE* 3.9 16.5 - - + +
40B VAL* 1.3 76.6 - - - +
42B LYS* 1.3 65.5 + - - +
50B ASP* 5.1 4.5 - - - +
54B ARG* 5.2 5.5 - - + +
113B TYR* 4.2 17.2 - - + -
114B VAL 3.2 7.1 + - - +
115B ALA* 3.2 25.3 - - + +
116B TYR* 3.3 11.0 + - - -
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Residues in contact with LYS 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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11B GLN* 3.6 19.4 + - - -
41B GLU* 1.3 75.8 - - - +
43B ALA* 1.3 69.5 + - - +
46B ALA* 4.3 9.2 - - + -
48B VAL 4.8 7.0 - - - +
50B ASP* 4.4 12.0 + - - +
115B ALA* 4.8 0.4 - - - +
116B TYR* 3.4 35.5 + - + +
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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