Contacts of the strand formed by residues 55 - 63 (chain B) in PDB entry 3C5C
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 ASP 55 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53B LEU* 4.1 16.0 + - + +
54B GLU* 1.3 80.6 - - - +
56B THR* 1.3 75.6 + - - +
57B TYR* 3.3 26.6 - - + -
73B MET* 4.5 2.5 - - - -
74B ASP 3.0 27.1 + - - -
203B MG 2.1 32.2 - - - -
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Residues in contact with THR 56 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141A TYR* 3.2 28.1 + - - +
55B ASP* 1.3 87.6 + - - +
57B TYR* 1.3 65.1 + - - +
58B SER* 4.2 4.6 + - - +
71B ARG* 3.7 24.9 - - + -
72B VAL 3.2 12.8 - - - +
73B MET* 3.6 25.6 - - - +
90B TRP* 4.1 4.9 - - + -
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Residues in contact with TYR 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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37B THR* 4.0 12.8 - - + -
38B VAL* 5.8 4.0 - - + -
41B LEU* 3.6 36.3 - - + +
49B TYR* 2.6 38.7 + + - -
53B LEU* 3.7 13.9 + - + +
55B ASP* 3.3 28.4 + - + -
56B THR* 1.3 74.8 - - - +
58B SER* 1.3 63.2 + - - +
59B SER* 5.2 0.5 - - - -
70B LEU 3.6 0.9 - - - +
71B ARG* 3.4 3.2 - - - -
72B VAL* 2.8 47.8 + - + +
74B ASP* 3.8 18.6 + - + -
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Residues in contact with SER 58 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141A TYR* 5.9 0.5 - - - -
41B LEU* 4.8 3.8 - - - +
56B THR* 4.2 4.8 + - - +
57B TYR* 1.3 75.0 - - - +
59B SER* 1.3 65.1 + - - +
70B LEU 3.2 7.0 - - - -
71B ARG* 3.8 18.4 + - - +
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Residues in contact with SER 59 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40B PHE* 4.8 2.7 - - - -
41B LEU* 4.0 22.6 - - - +
57B TYR 5.2 0.9 - - - -
58B SER* 1.3 77.0 - - - +
60B GLU* 1.3 63.6 + - - +
61B GLU* 2.7 31.0 + - - -
69B HIS* 3.6 2.3 - - - -
70B LEU* 2.7 47.5 + - - +
72B VAL* 6.0 0.7 - - - -
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Residues in contact with GLU 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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59B SER* 1.3 73.7 + - - +
61B GLU* 1.3 65.7 + - - +
68B VAL 3.5 4.0 - - - +
69B HIS* 3.3 34.4 - - + +
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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
----------------------------------------------------------
40B PHE* 3.6 28.4 - - + +
41B LEU* 6.0 0.2 - - - -
59B SER* 2.7 25.1 + - - +
60B GLU* 1.3 78.5 - - - +
62B THR* 1.3 62.3 + - - +
63B VAL* 4.7 2.7 - - + -
67B PRO* 3.4 5.4 - - - +
68B VAL* 2.7 45.8 + - + +
70B LEU* 4.0 20.9 - - + -
173B GLN* 4.7 3.8 - - - +
177B HIS* 3.2 26.9 + - + +
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Residues in contact with THR 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 78.0 + - - +
63B VAL* 1.3 66.4 + - - +
65B HIS* 3.4 15.5 - - - +
66B GLN 3.2 35.2 - - - +
67B PRO* 4.2 3.3 - - - +
177B HIS* 3.4 15.1 + - - -
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Residues in contact with VAL 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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61B GLU* 4.7 3.4 - - + -
62B THR* 1.3 75.8 - - - +
64B ASP* 1.3 77.3 + - + +
65B HIS 3.2 0.2 - - - -
66B GLN* 2.8 23.6 + - - +
68B VAL* 4.0 20.3 - - + +
177B HIS* 3.2 61.0 - - + +
180B VAL* 4.0 19.1 - - + -
181B ARG* 4.0 20.2 - - + +
184B ARG* 4.5 4.9 + - - +
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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