Contacts of the strand formed by residues 54 - 59 (chain B) in PDB entry 5N2F
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 54 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119A GLY 4.2 3.1 - - - +
120A GLY* 3.9 10.5 - - - -
121A ALA* 3.8 30.7 - - + +
52B ALA 5.2 0.2 - - - +
53B LEU* 1.3 79.7 - - - +
55B VAL* 1.3 64.1 + - - +
56B TYR 4.2 0.2 - - - -
67B PHE 3.3 7.4 - - - +
68B VAL* 4.1 14.8 - - + -
69B HIS* 3.6 24.7 - - + +
116B ILE* 3.3 8.8 - - - +
117B SER* 2.9 45.3 + - - +
201B 8HW 3.4 44.2 - - + -
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Residues in contact with VAL 55 (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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42B PHE* 4.9 0.2 - - + -
53B LEU* 3.8 23.1 - - + -
54B ILE* 1.3 78.6 - - - +
56B TYR* 1.3 64.5 + - - +
57B TRP* 4.0 19.3 - - + -
66B GLN* 3.1 7.3 - - - +
67B PHE* 2.8 36.7 + - + +
87B LEU* 3.9 25.6 - - + -
92B LEU* 4.0 20.9 - - + -
97B ALA* 4.1 19.7 - - + -
114B CYS* 5.2 0.9 - - - -
115B MET 3.6 4.9 - - - +
116B ILE* 4.5 8.3 - - + -
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Residues in contact with TYR 56 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123A TYR* 3.5 18.9 + + - -
55B VAL* 1.3 75.3 - - - +
57B TRP* 1.3 67.3 + - - +
58B GLU* 3.5 29.0 - - + +
62B LYS 4.6 0.2 - - - -
63B ASN* 2.5 31.1 + - + -
65B ILE 3.7 11.4 - - - -
66B GLN* 3.9 7.2 - - + -
113B ARG 3.7 0.5 - - - +
114B CYS* 3.8 1.6 - - - -
115B MET* 2.8 71.5 + - + +
201B 8HW 3.4 64.8 - + + +
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Residues in contact with TRP 57 (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 ILE* 3.4 44.4 - - + -
40B CYS* 3.5 6.5 - - + -
55B VAL* 4.0 18.3 - - + +
56B TYR* 1.3 79.3 - - - +
58B GLU* 1.3 61.2 + - - +
63B ASN 3.9 0.2 - - - -
64B ILE* 2.9 32.5 + - + +
65B ILE* 3.0 37.1 + - + +
87B LEU* 4.2 4.2 - - + +
97B ALA 3.0 29.7 + - - -
99B LEU* 3.6 25.9 - - + +
112B TYR* 4.3 10.1 - + + -
113B ARG 3.4 17.9 - - - -
114B CYS* 3.5 35.4 - - + -
126B ILE* 3.8 17.9 - - + -
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Residues in contact with GLU 58 (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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113A ARG* 3.1 30.3 + - - -
123A TYR* 2.2 38.9 + - - -
56B TYR* 3.5 20.0 - - + +
57B TRP* 1.3 75.5 - - - +
59B MET* 1.3 61.0 + - - +
61B ASP* 3.9 8.7 + - - -
62B LYS 3.1 16.6 - - - +
64B ILE* 3.5 6.6 - - - +
112B TYR* 3.3 5.2 - - - +
113B ARG* 2.8 61.0 + - + +
115B MET* 4.9 2.5 - - + -
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Residues in contact with MET 59 (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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58B GLU* 1.3 76.6 - - - +
60B GLU* 1.3 81.8 + - + +
61B ASP 3.2 0.9 - - - -
62B LYS* 2.9 51.4 + - + +
64B ILE* 3.6 7.3 - - + +
81B TYR* 3.6 20.2 - - + +
107B GLN 4.1 11.0 - - - +
108B ASP 3.9 8.5 - - - +
109B ALA 4.0 13.7 - - - +
110B GLY* 4.1 4.3 - - - -
111B VAL 3.2 23.1 - - - +
112B TYR* 3.7 34.8 - - + -
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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