Contacts of the strand formed by residues 5 - 10 (chain G) in PDB entry 1OQE
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 CYS 5 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3G GLN 3.6 10.8 - - - -
4G ASP* 1.3 80.0 - - - +
6G LEU* 1.3 61.9 + - - +
31G PHE* 3.7 26.4 - - + -
32G LYS* 3.7 1.2 - - - +
33G ARG* 2.8 45.0 + - - +
37G LEU* 3.8 6.9 - - - +
140G ALA 3.1 16.2 - - - +
141G LEU* 3.8 11.9 - - + -
51I TYR* 5.3 0.4 - - - -
109I ILE* 4.2 14.8 - - + -
143I LEU* 4.3 12.1 - - - -
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Residues in contact with LEU 6 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5G CYS* 1.3 76.0 - - - +
7G GLN* 1.3 60.6 + - - +
8G LEU* 3.4 32.5 - - + -
29G LEU* 4.3 5.4 - - + -
31G PHE* 3.5 11.4 - - - +
32G LYS* 4.0 13.7 - - + -
37G LEU* 3.6 21.9 - - + +
38G GLU* 3.4 40.8 - - - +
39G GLU* 3.6 7.9 - - + +
44G ILE* 4.2 21.6 - - + +
55G TYR* 5.0 0.7 - - - -
139G GLY* 3.2 3.1 - - - -
140G ALA 3.0 30.7 + - - -
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Residues in contact with GLN 7 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6G LEU* 1.3 75.0 - - - +
8G LEU* 1.3 74.9 + - - +
9G ILE* 5.0 3.8 - - - +
29G LEU* 3.7 0.5 - - - +
30G SER* 2.8 42.2 + - - -
31G PHE* 3.0 32.1 + - + +
55G TYR* 2.7 35.3 + - + +
137G PHE* 5.0 6.8 - - + -
138G PHE 3.6 6.7 - - - +
89I PHE* 4.4 9.3 - - - -
108I GLY* 3.8 3.6 - - - -
109I ILE* 2.9 42.9 - - - +
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Residues in contact with LEU 8 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6G LEU* 3.4 17.3 - - + -
7G GLN* 1.3 85.7 - - - +
9G ILE* 1.3 63.4 + - - +
27G TRP* 3.7 42.0 - - + -
28G LEU 3.5 1.8 - - - +
29G LEU* 4.0 19.7 - - + -
39G GLU* 4.3 14.1 - - + +
42G ASN 5.2 1.1 - - - +
43G LYS 4.8 8.5 - - - +
44G ILE* 3.6 33.0 - - + -
137G PHE* 3.3 8.0 - - - +
138G PHE* 2.6 42.2 + - + +
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Residues in contact with ILE 9 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7G GLN* 5.0 4.3 - - - +
8G LEU* 1.3 78.3 - - - +
10G ALA* 1.3 74.8 + - - +
27G TRP* 3.4 6.1 - - - -
28G LEU* 2.8 48.0 + - + +
29G LEU 5.7 0.4 - - - +
30G SER* 3.6 26.9 - - - +
133G GLY* 3.2 37.5 - - - +
136G THR 4.1 2.0 - - - -
137G PHE* 4.1 7.9 - - + -
88I LEU 5.9 1.6 - - - +
89I PHE* 6.4 2.0 - - + -
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Residues in contact with ALA 10 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9G ILE* 1.3 86.5 - - - +
11G ASP* 1.3 59.5 + - - +
12G SER 3.6 0.7 + - - -
25G VAL* 4.0 10.1 - - + -
26G PRO 3.6 5.8 - - - -
27G TRP* 3.5 5.6 - - - -
28G LEU* 4.7 1.4 - - - +
131G LEU* 3.4 35.4 - - + +
132G ASP 4.2 2.2 - - - +
133G GLY* 4.2 3.1 + - - -
136G THR* 3.0 36.6 + - - +
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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