Contacts of the strand formed by residues 19 - 25 (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 CYS 19 (chain c).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16c GLY* 3.1 20.4 + - - -
17c LYS* 3.6 17.9 - - - -
18c ASN* 1.3 79.4 - - - +
20c VAL* 1.3 64.8 + - - +
112c LEU* 4.2 4.7 - - - -
119c PRO* 3.6 8.7 - - - +
158c MET 4.0 2.7 - - - -
160c PRO* 4.0 25.4 - - + -
163c LEU* 3.7 20.0 - - - -
189c ILE* 4.0 10.1 - - + -
190c ILE 3.4 14.6 - - - +
191c GLU* 4.1 14.6 - - + +
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Residues in contact with VAL 20 (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 3.3 14.4 - - - +
15c LYS* 4.0 5.4 - - - -
19c CYS* 1.3 77.7 - - - +
21c ALA* 1.3 64.0 + - - +
110c ALA* 4.2 7.6 - - + -
111c GLY* 4.0 14.8 - - - +
112c LEU* 4.1 6.5 - - + -
119c PRO* 4.1 13.2 - - + -
120c PHE 4.2 6.1 - - - +
121c ILE* 3.6 26.0 - - + -
163c LEU* 3.8 5.2 - - - -
188c HIS 4.2 0.2 - - - +
189c ILE* 3.3 2.4 - - - +
190c ILE* 2.8 58.1 + - + +
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Residues in contact with ALA 21 (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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13c ALA* 3.2 4.2 - - - +
14c MET 2.8 35.5 + - - +
20c VAL* 1.3 76.8 - - - +
22c ILE* 1.3 63.1 + - - +
110c ALA* 4.2 4.5 - - - +
163c LEU* 3.8 23.1 - - + -
167c ILE* 3.6 24.0 - - + -
187c VAL* 4.9 0.9 - - + -
188c HIS 3.3 11.0 - - - +
189c ILE* 4.2 8.5 - - + -
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Residues in contact with ILE 22 (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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11c VAL* 4.3 4.7 - - + -
12c MET 3.1 13.0 - - - +
13c ALA* 4.2 5.8 - - + -
21c ALA* 1.3 75.4 - - - +
23c ALA* 1.3 63.4 + - - +
42c ILE* 3.8 25.0 - - + +
50c TYR* 4.3 17.9 - - + +
51c ILE 4.0 5.2 - - - -
52c GLY* 3.6 35.7 - - - +
108c VAL* 4.0 8.5 - - + +
110c ALA* 3.9 13.7 - - + -
167c ILE* 4.1 1.6 - - - -
187c VAL* 3.6 0.7 - - - -
188c HIS* 2.9 44.8 + - + +
190c ILE* 6.2 0.9 - - + -
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Residues in contact with ALA 23 (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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11c VAL* 3.3 1.9 - - - +
12c MET 2.7 34.1 + - - +
22c ILE* 1.3 75.2 - - - +
24c ALA* 1.3 67.0 + - - +
42c ILE* 3.8 3.6 - - - +
167c ILE* 4.0 11.2 - - + +
171c MET* 3.6 29.1 - - + +
185c VAL* 4.5 0.9 - - + -
186c ILE 3.2 12.3 - - - +
187c VAL* 3.9 15.9 - - + -
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Residues in contact with ALA 24 (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 3.2 16.2 - - - +
11c VAL* 3.9 10.5 - - + -
23c ALA* 1.3 76.7 - - - +
25c ASP* 1.3 70.9 + - - +
41c LYS* 4.3 8.7 - - + -
42c ILE* 3.5 22.7 - - + -
171c MET* 3.9 8.4 - - - +
185c VAL* 4.3 0.4 - - - +
186c ILE* 2.9 36.7 + - + +
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Residues in contact with ASP 25 (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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9c GLY* 3.7 2.0 - - - -
10c ALA 3.0 25.0 + - - +
24c ALA* 1.3 81.2 - - - +
26c ARG* 1.3 61.4 + - - +
27c ARG* 3.7 7.1 + - - +
39c PHE 4.4 1.6 - - - +
41c LYS* 2.8 45.9 + - - +
171c MET* 3.9 3.4 - - + +
175c VAL* 4.6 10.3 - - + -
180c VAL 4.3 0.3 - - - +
181c SER* 3.4 10.5 - - - -
182c GLY* 2.9 38.1 + - - +
184c GLY 3.3 9.6 - - - +
185c VAL* 4.4 1.6 - - + +
186c ILE* 4.9 1.6 - - - +
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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