Contacts of the strand formed by residues 80 - 88 (chain B) in PDB entry 1N54
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 ALA 80 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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48B SER 5.0 2.0 - - - +
49B PHE* 3.2 50.9 - - - +
51B THR 5.3 3.8 - - - +
71B MET* 5.2 13.9 - - + -
72B GLY 3.5 8.1 - - - -
73B LEU* 4.6 1.4 - - - +
74B ASP* 5.7 0.2 - - - -
79B THR* 1.3 74.8 + - - +
81B CYS* 1.3 63.3 + - - +
82B GLY 3.4 3.0 + - - +
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Residues in contact with CYS 81 (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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49B PHE* 3.5 18.3 - - - -
72B GLY 3.2 10.6 + - - +
73B LEU 3.4 29.4 - - - +
74B ASP* 3.9 19.3 - - - +
79B THR 2.9 4.1 + - - -
80B ALA* 1.3 72.7 - - - +
82B GLY* 1.3 57.2 + - - +
83B PHE* 4.2 14.8 - - + -
126B GLY* 3.9 20.6 - - - -
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Residues in contact with GLY 82 (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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46B ASN* 3.0 25.9 + - - -
47B LEU* 3.0 25.5 + - - -
48B SER 5.6 1.3 - - - -
49B PHE* 4.3 9.6 - - - -
80B ALA* 3.4 5.6 + - - +
81B CYS* 1.3 80.9 - - - +
83B PHE* 1.3 65.0 + - - +
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Residues in contact with PHE 83 (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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43B TYR* 3.7 27.6 - + + +
44B VAL 3.2 16.8 - - - +
45B GLY* 3.9 7.2 - - - -
46B ASN 4.6 0.2 - - - +
47B LEU* 3.7 16.4 - - - +
71B MET* 4.0 5.0 - - - +
72B GLY* 3.0 42.6 + - - +
73B LEU 4.4 7.6 - - - -
81B CYS* 4.2 22.0 - - + -
82B GLY* 1.3 81.8 + - - +
84B CYS* 1.3 86.9 - - - +
85B PHE* 4.1 17.0 - + - -
123B ARG 4.4 12.3 - - - -
124B GLN* 4.5 5.2 - - - -
125B TYR 4.7 1.1 - - - -
126B GLY* 4.6 9.6 - - - -
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Residues in contact with CYS 84 (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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43B TYR* 3.8 4.3 - - - -
44B VAL* 2.8 40.0 + - - +
47B LEU* 4.0 7.0 - - + -
56B ILE* 3.3 31.2 - - + -
69B ILE* 4.0 11.7 - - - -
70B ILE 3.3 17.7 - - - +
71B MET* 3.9 9.9 - - - -
72B GLY 3.9 0.2 - - - +
83B PHE* 1.3 89.4 - - - +
85B PHE* 1.3 62.6 + - - +
86B VAL* 4.1 13.2 - - - -
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Residues in contact with PHE 85 (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 THR* 4.3 11.4 - - - +
42B LEU 3.5 5.4 - - - +
43B TYR* 3.7 28.5 - + - -
68B LYS 3.7 1.9 - - - +
69B ILE* 3.3 7.6 - - - +
70B ILE* 3.0 50.7 + - + +
83B PHE* 4.1 14.8 - + - -
84B CYS* 1.3 80.1 - - - +
86B VAL* 1.3 63.1 + - - +
87B GLU 4.1 0.4 - - - -
116B ASP* 3.6 35.9 - - + -
118B GLY 5.3 1.3 - - - -
119B PHE* 4.6 22.0 - + + -
123B ARG* 3.8 49.4 - - + -
124B GLN* 5.0 0.4 - - - -
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Residues in contact with VAL 86 (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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40B CYS 3.5 2.8 - - - +
41B THR* 3.2 4.0 + - - -
42B LEU* 2.9 40.8 + - + +
44B VAL* 3.6 22.2 - - + -
56B ILE* 4.1 12.3 - - + -
60B PHE* 3.7 34.8 - - + -
66B ILE* 3.7 23.8 - - + -
68B LYS 4.0 2.2 - - - -
69B ILE* 4.5 5.6 - - + +
84B CYS* 4.1 10.5 - - - -
85B PHE* 1.3 77.4 - - - +
87B GLU* 1.3 60.2 + - - +
88B TYR* 3.9 11.8 + - + -
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Residues in contact with GLU 87 (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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1556A GOL 5.7 0.3 - - - -
40B CYS* 3.6 7.6 - - + +
41B THR* 3.8 20.1 + - - +
66B ILE* 3.3 6.0 - - - +
67B LYS* 2.6 71.7 + - + +
68B LYS* 3.1 23.7 + - + +
70B ILE* 5.7 5.0 - - + +
85B PHE 4.1 0.4 - - - -
86B VAL* 1.3 72.4 - - - +
88B TYR* 1.3 63.4 - - - +
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Residues in contact with TYR 88 (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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40B CYS* 2.9 27.2 + - - +
42B LEU* 4.0 12.1 - - + -
60B PHE* 3.0 40.0 + + + +
63B SER* 2.9 13.2 + - - -
64B GLY 3.2 17.7 - - - -
65B ASP 3.5 12.1 - - - -
66B ILE* 4.0 8.1 - - + -
67B LYS* 4.2 2.5 - - - +
86B VAL* 4.3 12.6 - - + -
87B GLU* 1.3 85.0 - - - +
89B TYR* 1.3 64.9 + - - +
90B SER 3.5 15.9 - - - +
93B ASP* 3.9 9.9 - - + -
94B ALA* 3.4 31.4 - - + +
97B ALA* 2.7 30.0 - - + +
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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