Contacts of the strand formed by residues 119 - 124 (chain q) 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 PRO 119 (chain q).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15q LYS* 3.2 39.8 - - + -
16q GLY 4.4 2.9 - - - +
17q LYS 3.9 22.4 - - - +
18q ASN* 4.6 4.3 - - - +
19q CYS 3.5 23.1 - - - +
20q VAL* 4.2 4.0 - - + -
112q LEU* 3.5 15.7 - - + -
117q PHE* 3.3 8.0 - - + +
118q LYS* 1.3 105.7 + - + +
120q PHE* 1.3 58.1 + - - +
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Residues in contact with PHE 120 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15q LYS* 4.7 2.2 - - - +
20q VAL* 4.0 1.0 - - - +
84q PRO* 3.5 42.4 - - + -
85q TYR* 3.3 43.3 - + - -
88q MET* 4.1 8.5 - - + -
109q ILE* 4.2 14.4 - - + -
110q ALA* 3.6 0.2 - - - -
111q GLY 2.9 36.3 + - - +
113q ASP* 5.7 0.7 - - + +
118q LYS 4.6 3.4 - - - +
119q PRO* 1.3 74.2 - - - +
121q ILE* 1.3 70.3 + - - +
122q CYS* 3.8 26.9 - - + -
132q VAL* 3.6 27.4 - - + -
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Residues in contact with ILE 121 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13q ALA* 4.0 20.0 - - + +
14q MET 4.1 3.6 - - - +
15q LYS* 4.1 10.8 - - + +
20q VAL* 3.5 23.6 - - + -
109q ILE 3.2 7.4 - - - +
110q ALA* 4.3 1.6 - - + -
120q PHE* 1.3 83.0 - - - +
122q CYS* 1.3 65.5 + - - +
132q VAL* 3.7 6.4 - - - +
133q THR* 3.3 52.5 + - - +
135q ASP 3.6 11.9 - - - +
136q PHE* 3.6 26.9 - - - +
137q VAL* 4.1 7.2 - - + -
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Residues in contact with CYS 122 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88q MET* 3.5 31.9 - - - -
108q VAL* 3.3 8.0 - - - +
109q ILE* 2.8 54.7 + - - +
120q PHE* 3.8 5.4 - - + -
121q ILE* 1.3 78.8 - - - +
123q SER* 1.3 64.0 + - - +
124q LEU* 4.1 6.5 - - - -
131q MET 3.3 14.4 - - - +
132q VAL* 3.6 16.2 - - + -
137q VAL* 3.8 8.2 - - - +
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Residues in contact with SER 123 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107q PRO 3.2 12.6 - - - -
108q VAL* 3.9 13.2 - - - -
122q CYS* 1.3 78.1 - - - +
124q LEU* 1.3 71.0 + - - +
131q MET* 3.0 57.6 + - - +
137q VAL* 4.0 14.8 - - - +
138q VAL 4.2 4.9 + - - -
139q SER* 4.2 9.0 - - - -
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Residues in contact with LEU 124 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88q MET* 3.8 13.0 - - + +
91q VAL* 4.1 13.2 - - + -
92q ALA* 3.6 42.4 - - + +
95q LEU* 4.4 0.4 - - + -
106q GLU* 3.5 23.4 - - - +
107q PRO* 3.0 36.9 + - + +
109q ILE* 4.7 5.6 - - + -
122q CYS* 4.1 15.7 - - - -
123q SER* 1.3 85.1 - - - +
125q ASP* 1.3 69.5 + - - +
128q GLY* 4.0 11.7 - - - +
129q CYS 3.3 5.8 - - - +
130q PRO* 4.2 7.6 - - + -
131q MET* 5.9 2.2 - - - -
139q SER* 5.0 0.5 + - - -
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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