Contacts of the strand formed by residues 56 - 63 (chain A) in PDB entry 2COJ
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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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33A THR 3.8 14.6 - - - -
34A PRO* 3.5 7.3 - - + +
35A ALA* 3.0 29.6 + - - +
38A LEU* 3.9 12.8 - - + -
54A THR* 3.1 17.7 + - - -
55A ASP* 1.3 95.8 - - + +
57A MET* 1.3 63.0 + - - +
73A ILE* 4.1 7.6 - - + -
74A LYS 3.2 14.8 - - - +
75A PRO* 4.2 0.4 - - + -
76A LEU* 3.9 5.4 - - - +
144A LEU* 3.8 18.2 - - + +
147A LEU* 3.6 25.6 - - + +
148A ASP* 2.7 32.3 + - - +
185A VAL 4.9 0.2 - - - +
187A LEU* 4.5 5.2 + - - +
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Residues in contact with MET 57 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56A HIS* 1.3 75.5 - - - +
58A LEU* 1.3 59.3 + - - +
59A THR* 3.8 27.3 + - + -
72A HIS 3.8 0.2 - - - +
73A ILE* 3.2 6.9 - - - +
74A LYS* 2.8 40.9 + - + +
75A PRO 3.9 4.7 - - - +
76A LEU* 3.8 11.9 - - + -
77A GLN* 3.6 39.7 - - - +
79A LEU* 4.3 7.2 - - + -
144A LEU* 4.2 7.6 - - - -
184A PHE* 4.3 9.6 - - + -
185A VAL 3.5 12.8 - - - +
186A LEU* 3.9 21.5 - - + -
83B PRO* 4.0 15.3 - - + -
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Residues in contact with LEU 58 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25A PHE* 6.2 0.7 - - + -
30A LEU* 4.1 15.9 - - + -
57A MET* 1.3 73.5 - - - +
59A THR* 1.3 67.7 + - - +
60A VAL* 4.5 8.5 - - + -
71A PRO* 4.3 7.2 - - + -
72A HIS 3.0 28.5 - - - +
73A ILE* 3.9 14.4 - - + +
137A LEU* 4.6 9.0 - - + -
140A CYS* 3.9 30.3 - - + +
141A ILE* 4.7 1.6 - - + -
144A LEU* 4.0 15.0 - - + +
183A LEU* 5.0 2.5 - - + -
184A PHE* 2.8 28.3 - - - +
185A VAL* 2.8 35.9 + - + -
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Residues in contact with THR 59 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57A MET* 3.8 23.1 - - + -
58A LEU* 1.3 80.8 - - - +
60A VAL* 1.3 67.1 + - - +
61A GLU* 6.1 1.5 - - - +
71A PRO* 3.7 0.2 - - - +
72A HIS* 3.0 42.9 + - - +
74A LYS* 3.4 38.4 + - - +
79A LEU* 5.1 7.2 - - + -
182A LEU* 4.6 10.3 - - + -
183A LEU 3.2 7.4 - - - -
184A PHE* 3.9 6.3 - - + -
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Residues in contact with VAL 60 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25A PHE* 3.7 23.1 - - + -
58A LEU* 4.5 11.7 - - + -
59A THR* 1.3 84.1 - - - +
61A GLU* 1.3 63.5 + - - +
68A TRP* 3.5 30.6 - - + -
69A GLU 3.8 18.4 - - - +
70A LYS 4.9 1.6 - - - -
71A PRO* 3.6 23.6 - - + -
72A HIS* 6.0 0.4 - - - -
182A LEU* 3.6 5.2 - - - +
183A LEU* 2.7 45.8 + - + +
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Residues in contact with GLU 61 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59A THR* 6.1 1.3 - - - +
60A VAL* 1.3 76.0 - - - +
62A TRP* 1.3 61.7 + - - +
68A TRP* 3.7 3.9 - - - -
69A GLU* 2.8 48.2 + - + +
70A LYS 5.2 0.8 + - - -
169A THR* 4.9 3.5 + - - +
180A LYS* 5.2 6.9 - - - -
181A ALA 3.3 14.8 - - - +
182A LEU* 3.5 22.0 - - + +
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Residues in contact with TRP 62 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61A GLU* 1.3 76.8 + - - +
63A SER* 1.3 65.6 + - - +
64A SER* 3.5 28.5 - - - -
67A GLY* 3.3 33.7 - - - -
68A TRP* 3.4 40.8 - + + +
69A GLU* 5.2 0.7 - - - -
130A PRO* 3.5 32.7 - - + +
177A LYS* 4.4 12.3 - - - -
178A PRO* 3.5 15.9 - - + -
179A THR 3.4 23.1 - - - -
180A LYS* 3.3 8.2 - - - +
181A ALA* 2.9 55.2 + - + +
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Residues in contact with SER 63 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62A TRP* 1.3 80.8 - - - +
64A SER* 1.3 56.3 + - - +
65A GLU* 3.0 7.6 - - - -
66A PHE* 3.1 31.4 + - - +
67A GLY* 2.6 41.0 + - - -
69A GLU* 4.4 5.5 + - - -
179A THR 3.4 9.2 - - - -
180A LYS* 4.4 8.5 - - - +
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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