Contacts of the strand formed by residues 56 - 60 (chain B) in PDB entry 3C3C
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 SER 56 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16B LYS 3.9 0.4 + - - -
17B ARG* 3.3 26.0 - - - +
18B VAL* 2.9 25.5 + - - +
50B LEU* 5.3 1.3 - - - -
54B ALA* 3.4 4.6 - - - +
55B LYS* 1.3 78.8 - - - +
57B VAL* 1.3 68.8 + - - +
58B VAL* 4.9 4.8 - - - +
110B PRO* 3.8 32.9 - - - +
111B ALA 4.6 0.4 - - - -
113B GLY* 4.7 1.3 - - - -
114B SER* 3.4 16.8 - - - +
156B LEU 5.1 0.3 + - - -
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Residues in contact with VAL 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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18B VAL* 3.4 10.3 - - + +
20B MET* 4.4 19.5 - - + -
46B ILE* 4.6 19.3 - - + +
49B CYS* 3.7 28.7 - - + -
50B LEU* 4.5 12.8 - - + +
54B ALA* 4.5 3.4 - - + -
56B SER* 1.3 78.6 - - - +
58B VAL* 1.3 64.2 + - - +
59B LEU* 4.3 23.3 - - + -
114B SER 2.7 12.0 + - - +
115B VAL* 3.5 8.3 - - + +
116B ILE* 3.0 26.2 + - - +
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Residues in contact with VAL 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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18B VAL 2.9 12.6 + - - +
19B VAL* 3.4 8.9 - - + +
20B MET* 2.8 32.7 + - - +
56B SER* 4.9 7.9 - - - +
57B VAL* 1.3 75.3 - - - +
59B LEU* 1.3 60.3 + - - +
107B CYS* 4.4 13.9 - - + +
110B PRO* 4.9 0.7 - - + -
116B ILE* 3.6 26.7 - - + -
118B LEU* 3.9 31.2 - - + -
156B LEU* 3.9 38.1 - - + +
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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
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20B MET* 3.5 24.0 - - + +
22B VAL* 3.8 31.2 - - + -
24B PHE* 4.3 6.1 - - + -
46B ILE* 3.9 16.4 - - + -
57B VAL* 4.3 8.5 - - + -
58B VAL* 1.3 74.4 - - - +
60B MET* 1.3 59.0 + - - +
84B LEU* 3.7 30.5 - - + -
115B VAL* 3.9 14.6 - - + -
116B ILE 2.7 22.2 + - - +
117B LEU* 4.0 14.6 - - + -
118B LEU* 2.8 37.1 + - - +
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Residues in contact with MET 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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19B VAL* 3.9 24.5 - - + -
20B MET 3.2 10.7 + - - +
21B ARG* 3.6 15.4 - - + +
22B VAL* 3.0 28.2 + - - +
59B LEU* 1.3 75.4 - - - +
61B SER* 1.3 61.0 + - - +
117B LEU* 5.0 1.1 - - - -
118B LEU* 4.1 14.4 - - + +
121B LEU* 3.9 17.7 - - + -
153B LEU* 4.4 24.7 - - + -
156B LEU* 4.9 3.6 - - - -
160B TYR* 3.8 29.4 - - + -
174B SER* 3.8 22.2 - - - +
178B VAL* 4.0 9.9 - - + -
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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