Contacts of the strand formed by residues 57 - 64 (chain B) in PDB entry 4PAR
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 ILE 57 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49B PHE* 3.9 22.0 - - + -
50B VAL 3.7 11.0 - - - +
51B ARG* 4.8 11.2 - - - +
55B LYS 4.4 7.0 - - - +
56B LYS* 1.3 75.0 - - - +
58B ALA* 1.3 68.5 + - - +
98B SER* 3.8 1.6 - - - -
99B ILE* 2.9 35.3 + - + +
104B SER* 3.4 48.9 + - - +
107B MET* 4.5 5.8 - - + +
108B ARG* 5.1 1.6 - - + +
112B ILE* 3.6 31.4 - - + -
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Residues in contact with ALA 58 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49B PHE* 3.3 5.9 - - - +
50B VAL* 2.9 30.8 + - + +
52B LEU* 3.7 24.7 - - + -
56B LYS 3.7 0.6 + - - -
57B ILE* 1.3 78.7 - - - +
59B LEU* 1.3 66.3 + - - +
95B PRO* 3.6 21.8 - - + -
97B TYR 3.3 20.4 - - - +
98B SER* 4.2 1.3 - - - +
99B ILE* 4.6 2.2 - - - +
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Residues in contact with LEU 59 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B ASN* 3.8 26.2 - - - +
23B LYS* 5.0 3.7 + - - -
47B GLN* 4.4 12.8 - - + +
48B GLN 3.1 18.2 - - - +
49B PHE* 4.2 13.5 - - + +
50B VAL* 4.3 1.3 - - - +
58B ALA* 1.3 79.9 - - - +
60B THR* 1.3 74.2 + - - +
61B ASP* 4.7 9.0 - - - +
72B GLU* 4.7 4.0 - - - +
85B MET* 3.7 30.1 - - + -
95B PRO* 3.7 13.0 - - - +
97B TYR* 3.7 9.6 + - + +
99B ILE* 4.5 21.1 - - + -
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Residues in contact with THR 60 (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 LYS* 5.9 0.2 - - - +
47B GLN* 3.2 5.0 - - - -
48B GLN* 2.9 36.0 + - - +
50B VAL* 4.6 5.6 - - + -
59B LEU* 1.3 81.1 - - - +
61B ASP* 1.3 66.7 + - - +
62B LEU 4.3 0.5 + - - -
63B TYR* 4.1 2.9 - - - +
70B HIS* 2.5 53.0 + - + +
71B ILE 4.3 5.4 - - - -
72B GLU* 5.1 6.7 - - + -
95B PRO* 4.0 20.9 - - + -
115B ILE* 5.5 0.2 - - + -
120B ILE* 4.1 8.7 - - + -
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Residues in contact with ASP 61 (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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22B ASN* 5.6 1.2 + - - +
23B LYS* 2.4 46.8 + - - +
26B GLU* 3.9 23.4 - - + +
30B VAL* 4.2 19.5 - - + +
46B THR* 3.2 12.6 - - - +
47B GLN* 3.2 20.9 + - - +
59B LEU* 4.7 5.2 - - - +
60B THR* 1.3 75.6 - - - +
62B LEU* 1.3 60.5 + - - +
71B ILE* 3.2 11.0 + - + +
72B GLU* 3.4 1.1 - - - +
73B VAL* 2.6 25.2 + - + +
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Residues in contact with LEU 62 (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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30B VAL* 4.0 28.5 - - + -
33B ILE* 3.7 27.1 - - + -
34B ILE* 3.9 8.3 - - + -
44B PHE* 3.6 35.4 - - + -
45B VAL 3.4 5.4 - - - +
46B THR* 4.2 2.7 - - + -
60B THR* 4.3 1.5 + - - -
61B ASP* 1.3 77.3 - - - +
63B TYR* 1.3 66.0 + - - +
64B PHE* 3.6 32.1 - - + -
69B ILE 3.9 0.5 - - - +
70B HIS* 3.3 4.5 - - - +
71B ILE* 2.8 48.4 + - + +
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Residues in contact with TYR 63 (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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44B PHE* 3.2 1.0 - - - -
45B VAL* 2.6 45.1 + - + +
48B GLN* 3.4 34.8 - - + -
60B THR* 4.1 0.2 - - - +
62B LEU* 1.3 75.9 - - - +
64B PHE* 1.3 74.6 + - - +
65B PRO* 3.2 43.8 + - + +
68B GLY* 4.2 1.1 - - - -
69B ILE 3.2 17.5 - - - -
70B HIS* 3.2 36.1 - + - +
113B ILE* 3.5 22.0 - - + +
118B HIS* 3.5 20.4 + - - -
188B ASN* 4.7 6.9 + - - -
286B ARG* 6.3 0.7 - - - -
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Residues in contact with PHE 64 (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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33B ILE* 4.7 0.7 - - + -
34B ILE* 4.1 9.0 - - + -
37B LEU* 3.8 28.0 - - + -
39B ASP 5.8 0.4 - - - -
42B LEU* 4.3 21.5 - - + -
43B LYS 3.3 18.8 - - - +
44B PHE* 3.6 15.7 - + + -
62B LEU* 3.6 33.7 - - + -
63B TYR* 1.3 73.8 - - - +
65B PRO* 1.3 63.6 - - - +
66B GLN* 3.4 0.9 - - + +
67B LEU* 3.4 21.7 + - + -
68B GLY 2.9 22.2 + - - -
69B ILE* 2.9 30.4 + - + +
71B ILE* 4.0 5.6 - - + -
150B ILE* 3.5 26.0 - - + -
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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