Contacts of the strand formed by residues 10 - 15 (chain c) in PDB entry 5GJQ
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 ALA 10 (chain c).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9c GLY* 1.3 74.3 - - - -
11c VAL* 1.3 68.0 - - - +
24c ALA* 3.2 23.6 - - - +
25c ASP* 3.0 10.8 + - - +
41c LYS* 4.2 1.3 - - - +
54c ALA* 4.3 1.8 - - - +
139c SER 3.5 5.8 - - - -
140c GLY* 4.3 0.2 - - - -
142c CYS* 3.5 30.3 - - - -
146c MET* 4.2 8.3 - - - -
171c MET* 4.2 5.6 - - + -
175c VAL* 4.1 14.4 - - + -
181c SER* 4.1 3.8 - - - +
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Residues in contact with VAL 11 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10c ALA* 1.3 81.6 - - - +
12c MET* 1.3 63.1 + - - +
22c ILE* 4.3 7.0 - - + -
23c ALA 3.3 7.9 - - - +
24c ALA* 3.9 13.5 - - + -
41c LYS* 4.8 3.8 - - + +
52c GLY* 3.7 15.0 - - - -
53c LEU 4.0 23.1 - - - +
54c ALA* 4.0 15.5 - - + +
108c VAL* 3.6 33.7 - - + -
138c VAL* 3.4 3.6 - - - +
139c SER* 2.8 37.6 + - - +
146c MET* 4.0 4.1 - - - +
171c MET* 4.9 0.2 - - - -
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Residues in contact with MET 12 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11c VAL* 1.3 77.0 - - - +
13c ALA* 1.3 70.7 + - - +
14c MET* 3.8 4.3 - - + -
22c ILE* 3.1 5.8 - - - +
23c ALA 2.7 36.2 + - - +
136c PHE* 5.2 0.2 - - + -
137c VAL 3.4 9.6 - - - +
138c VAL* 3.9 7.9 - - + +
146c MET* 3.7 26.0 - - + -
150c CYS* 3.4 29.8 - - - -
167c ILE* 3.7 25.1 - - + +
170c ALA* 3.8 7.6 - - + -
171c MET* 3.5 44.4 - - + +
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Residues in contact with ALA 13 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12c MET* 1.3 77.8 - - - +
14c MET* 1.3 61.8 + - - +
21c ALA 3.2 11.0 - - - +
22c ILE* 4.2 2.2 - - + -
108c VAL* 3.5 24.9 - - + +
110c ALA* 4.0 17.5 - - + -
121c ILE* 4.0 6.5 - - + -
136c PHE* 3.2 8.8 - - - +
137c VAL* 2.8 39.7 + - + +
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Residues in contact with MET 14 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12c MET* 3.8 14.6 - - - -
13c ALA* 1.3 75.1 - - - +
15c LYS* 1.3 60.1 + - - +
20c VAL* 3.3 4.8 - - - +
21c ALA 2.8 38.3 + - - -
121c ILE* 4.2 2.4 - - - +
135c ASP 3.5 5.2 - - - +
136c PHE* 4.3 4.0 - - + -
150c CYS* 3.5 33.9 - - + -
154c TRP* 3.6 24.0 - - + -
158c MET* 5.4 0.2 - - - +
163c LEU* 3.7 21.1 - - + +
166c THR* 3.7 27.1 - - + +
167c ILE* 3.7 35.0 - - + -
170c ALA* 4.8 0.2 - - + -
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Residues in contact with LYS 15 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14c MET* 1.3 74.4 - - - +
16c GLY* 1.3 61.2 + - - +
20c VAL* 4.0 6.3 - - + -
118c LYS* 3.1 21.2 - - - +
119c PRO* 3.2 43.8 + - + -
120c PHE* 4.2 4.9 - - - +
121c ILE* 4.1 12.5 - - + +
133c THR 3.7 10.2 + - - +
134c ASP* 2.3 63.5 + - - +
135c ASP 2.9 11.0 + - - +
154c TRP* 3.2 22.7 + - + +
156c PRO 4.9 0.9 - - - +
158c MET* 4.9 1.2 - - - +
163c LEU* 3.5 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