Contacts of the strand formed by residues 57 - 65 (chain B) in PDB entry 1C9O
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 GLY 57 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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53B GLN* 3.6 9.0 - - - -
54B GLY* 2.9 29.5 + - - -
55B ASN 3.5 1.0 - - - -
56B ARG* 1.3 79.9 - - - +
58B PRO* 1.3 78.7 - - - +
59B GLN* 3.5 4.7 + - - +
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Residues in contact with PRO 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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26B VAL* 4.6 9.4 - - + -
27B PHE* 4.2 13.9 + - - +
51B ILE* 4.1 12.8 - - + -
52B VAL 3.3 7.9 - - - +
53B GLN* 3.2 23.9 - - - +
56B ARG 4.7 2.1 - - - +
57B GLY* 1.3 86.4 - - - +
59B GLN* 1.3 61.8 + - - +
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Residues in contact with GLN 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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50A GLU* 6.2 1.6 - - - +
52A VAL* 3.5 26.9 - - - +
61A ALA* 5.1 5.1 - - - +
26B VAL* 3.6 9.6 - - - +
27B PHE* 3.4 29.3 - - + +
29B HIS 6.2 0.2 - - - +
51B ILE* 3.6 3.3 - - - -
52B VAL* 2.9 45.8 + - + +
54B GLY* 4.4 14.7 - - - -
55B ASN* 5.4 1.7 + - - +
56B ARG* 5.3 7.3 + - - +
57B GLY 4.3 4.3 - - - +
58B PRO* 1.3 78.3 - - - +
60B ALA* 1.3 65.8 + - - +
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Residues in contact with ALA 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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18B ILE* 3.9 12.1 - - + -
26B VAL* 3.6 2.9 - - + +
27B PHE 2.9 17.2 + - - +
28B VAL* 4.0 6.5 - - + -
29B HIS 5.3 2.1 + - - -
32B ALA* 3.5 14.6 - - - +
49B PHE* 3.8 17.5 - - + -
50B GLU 3.5 5.2 - - - -
52B VAL* 4.7 0.7 - - - +
59B GLN* 1.3 84.5 + - - +
61B ALA* 1.3 60.3 + - - +
63B VAL* 3.7 23.1 - - + -
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Residues in contact with ALA 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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52A VAL* 5.8 0.9 - - + -
59A GLN* 5.0 1.6 - - - +
61A ALA* 6.4 2.0 - - + -
32B ALA* 4.1 4.9 - - - -
49B PHE* 3.5 2.8 - - - +
50B GLU* 2.8 57.6 + - + +
52B VAL* 3.9 15.9 - - + -
60B ALA* 1.3 74.7 - - - +
62B ASN* 1.3 69.2 + - - +
63B VAL* 3.3 4.7 + - - -
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Residues in contact with ASN 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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29A HIS* 5.8 1.0 - - - -
31A THR* 3.7 26.3 + - - +
1B MET* 4.3 15.8 - - - +
32B ALA* 3.7 11.1 + - - +
34B GLN* 3.4 28.8 - - - +
48B SER* 3.4 10.4 + - - +
49B PHE* 3.5 4.2 - - - -
50B GLU* 2.8 27.7 - - + +
61B ALA* 1.3 71.7 - - + +
63B VAL* 1.3 61.7 + - - +
64B VAL* 3.4 11.2 + - - +
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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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18B ILE* 4.4 3.1 - - + -
28B VAL* 4.0 11.4 - - + -
32B ALA* 3.1 19.3 + - + +
33B ILE* 3.7 8.7 - - + +
34B GLN* 2.8 30.2 + - - +
41B LEU* 4.2 23.3 - - + -
47B VAL* 3.9 30.7 - - + -
48B SER 3.4 4.5 - - - -
49B PHE* 3.8 8.3 - - + -
60B ALA* 3.7 30.7 - - + -
61B ALA 3.9 1.8 - - - +
62B ASN* 1.3 69.8 - - - +
64B VAL* 1.3 61.9 + - - +
65B LYS* 4.2 0.9 + - - +
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Residues in contact with VAL 64 (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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34B GLN* 3.8 23.6 - - + -
47B VAL* 3.2 8.7 - - - -
48B SER* 2.9 48.1 + - - +
62B ASN* 3.9 14.6 - - - +
63B VAL* 1.3 76.7 - - - +
65B LYS* 1.3 72.7 + - - +
66B LEU* 3.5 7.9 + - + +
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Residues in contact with LYS 65 (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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33B ILE* 4.4 13.9 - - + -
34B GLN 5.2 6.3 + - - +
37B GLY* 6.2 0.2 - - - -
38B PHE 4.1 12.7 + - - -
40B THR* 2.7 36.7 + - - +
41B LEU* 3.9 23.3 - - + +
45B GLN* 3.7 25.4 - - - +
46B GLU 3.8 4.5 - - - -
47B VAL* 4.3 0.9 - - - -
63B VAL 4.2 0.8 + - - +
64B VAL* 1.3 82.4 - - - +
66B LEU* 1.3 60.4 + - - +
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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