Contacts of the strand formed by residues 56 - 63 (chain B) in PDB entry 2COI
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 HIS 56 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33B THR 4.3 0.2 + - - -
34B PRO* 3.5 12.6 - - + +
35B ALA* 2.8 42.9 + - + +
38B LEU* 4.7 7.0 - - + +
54B THR* 3.4 16.3 + - - +
55B ASP* 1.3 82.8 + - + +
57B MET* 1.3 64.0 + - - +
73B ILE* 4.2 4.2 - - + +
74B LYS* 3.2 11.7 + - - +
75B PRO* 3.8 10.7 - - - +
76B LEU* 3.8 7.1 - - - +
144B LEU* 3.7 22.6 - - + +
147B LEU* 3.3 30.0 + - + +
148B ASP* 2.7 36.4 + - - +
187B LEU 4.8 5.7 + - - -
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Residues in contact with MET 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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83A PRO* 3.8 15.7 - - + -
56B HIS* 1.3 77.5 - - - +
58B LEU* 1.3 59.7 + - - +
59B THR* 3.8 27.8 - - + -
72B HIS 3.6 0.5 - - - +
73B ILE* 3.4 4.0 - - - -
74B LYS* 2.8 44.6 + - + +
75B PRO 4.1 3.4 - - - +
76B LEU* 4.0 5.8 - - + -
77B GLN* 3.6 32.1 - - - +
79B LEU* 4.1 11.4 - - + -
144B LEU* 3.8 8.0 - - - +
184B PHE* 4.2 9.2 - - + -
185B VAL 3.4 13.9 - - - +
186B LEU* 3.7 26.0 - - + -
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Residues in contact with LEU 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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30B LEU* 3.9 25.1 - - + -
57B MET* 1.3 75.6 - - - +
59B THR* 1.3 62.3 + - - +
60B VAL* 3.5 22.4 - - + -
71B PRO* 4.1 6.3 - - + -
72B HIS 3.2 21.1 - - - +
73B ILE* 4.1 7.6 - - + +
137B LEU* 4.9 6.7 - - + -
140B CYS* 4.2 22.2 - - + +
141B ILE* 5.3 0.4 - - - +
144B LEU* 3.7 17.2 - - + +
183B LEU* 4.3 5.6 - - + +
184B PHE* 2.9 8.8 - - - +
185B VAL* 2.9 50.0 + - + -
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Residues in contact with THR 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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57B MET* 3.8 26.2 - - + -
58B LEU* 1.3 79.2 - - - +
60B VAL* 1.3 63.0 + - - +
61B GLU* 5.8 2.2 - - - -
70B LYS 4.3 1.0 - - - +
71B PRO* 3.8 0.2 - - - +
72B HIS* 2.9 45.0 + - - +
74B LYS* 3.1 37.5 + - - +
79B LEU* 4.9 8.3 - - + -
182B LEU* 4.3 11.9 - - + -
183B LEU 3.4 5.2 - - - -
184B PHE* 4.0 6.5 - - + -
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Residues in contact with VAL 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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25B PHE* 3.6 28.7 - - + -
58B LEU* 3.5 22.9 - - + -
59B THR* 1.3 80.5 - - - +
61B GLU* 1.3 62.0 + - - +
68B TRP* 3.5 30.4 - - + -
69B GLU 3.7 17.9 - - - +
70B LYS 4.4 2.2 - - - +
71B PRO* 4.0 18.4 - - + -
72B HIS* 6.1 0.2 - - - -
182B LEU* 3.4 5.7 - - - +
183B LEU* 2.7 41.0 + - + +
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Residues in contact with GLU 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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59B THR* 5.8 2.3 - - - -
60B VAL* 1.3 76.6 - - - +
62B TRP* 1.3 61.5 + - - +
68B TRP* 3.5 5.4 - - - -
69B GLU* 2.9 48.7 + - + +
70B LYS 5.1 0.4 + - - -
72B HIS* 6.4 1.8 - - + -
74B LYS* 5.9 1.2 + - - -
169B THR* 5.1 0.9 + - - +
180B LYS* 4.5 15.9 - - - -
181B ALA 3.7 12.3 - - - +
182B LEU* 3.5 23.1 - - + +
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Residues in contact with TRP 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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61B GLU* 1.3 77.3 - - - +
63B SER* 1.3 73.2 + - - +
64B SER* 3.6 21.1 - - - -
67B GLY* 3.4 34.9 - - - -
68B TRP* 3.4 42.4 - + + +
69B GLU* 5.9 0.2 - - - -
130B PRO* 3.5 38.3 - - + +
177B LYS* 5.5 7.6 - - - -
178B PRO 3.6 17.3 - - - -
179B THR 3.5 22.2 - - - -
180B LYS* 3.5 8.2 - - - +
181B ALA* 3.0 45.6 + - + +
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Residues in contact with SER 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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62B TRP* 1.3 85.1 - - - +
64B SER* 1.3 60.0 + - - +
65B GLU* 3.8 16.1 + - - -
66B PHE* 3.1 35.1 + - - +
67B GLY* 2.8 32.7 + - - -
69B GLU* 4.8 3.0 + - - -
179B THR 3.3 8.5 - - - -
180B LYS* 4.3 5.4 - - - +
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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