Contacts of the helix formed by residues 123 - 133 (chain V) 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 SER 123 (chain V).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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115V HIS* 4.5 5.2 + - - -
121V TRP* 3.3 24.5 - - - -
122V LEU* 1.3 75.7 - - - +
124V GLY* 1.3 59.3 + - - +
125V VAL* 3.4 12.4 + - - +
126V ASP* 2.8 48.7 + - - +
127V ILE* 2.8 11.8 + - - +
194V HIS* 5.1 2.7 - - - -
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Residues in contact with GLY 124 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122V LEU 3.9 0.4 + - - -
123V SER* 1.3 71.9 - - - +
125V VAL* 1.3 56.1 + - - +
127V ILE* 2.8 25.5 + - - +
128V ASN* 2.9 22.0 + - - +
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Residues in contact with VAL 125 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51L GLN* 5.7 4.3 - - - +
82V VAL 4.2 19.2 - - - +
83V SER* 4.7 10.5 - - - -
123V SER* 3.1 9.6 - - - +
124V GLY* 1.3 72.9 - - - +
126V ASP* 1.3 68.1 + - - +
128V ASN* 3.6 14.1 + - + +
129V THR* 3.4 21.8 + - - +
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Residues in contact with ASP 126 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52V GLU* 4.4 0.5 - - - +
82V VAL* 4.0 11.1 - - - +
111V TRP* 3.7 14.3 - - + -
113V HIS* 3.0 29.8 + - - -
115V HIS* 2.6 31.4 + - - -
122V LEU* 3.5 20.6 - - + -
123V SER* 2.8 36.1 + - - +
125V VAL* 1.3 78.5 - - - +
127V ILE* 1.3 61.3 + - - +
129V THR* 3.5 4.2 + - - -
130V GLN* 3.0 21.8 + - - +
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Residues in contact with ILE 127 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122V LEU* 4.6 9.6 - - + +
123V SER 2.8 8.4 + - - +
124V GLY* 2.8 20.7 + - - +
126V ASP* 1.3 74.6 - - - +
128V ASN* 1.3 72.9 + - - +
130V GLN* 2.8 20.5 + - - +
131V GLN* 2.9 24.7 + - + +
162V LEU* 4.9 11.4 - - + -
199V HIS* 5.9 8.3 - - + -
200V TYR* 5.9 4.9 - - + -
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Residues in contact with ASN 128 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84V VAL* 4.5 11.1 - - + +
124V GLY 2.9 19.4 + - - +
125V VAL* 4.1 16.4 - - + +
126V ASP 3.5 0.4 - - - -
127V ILE* 1.3 78.4 - - - +
129V THR* 1.3 64.0 + - - +
131V GLN* 3.0 23.6 + - - +
132V SER* 3.0 19.2 + - - -
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Residues in contact with THR 129 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54V MET* 5.0 2.5 - - - -
82V VAL* 5.5 0.2 - - - +
83V SER* 3.7 11.2 - - - +
84V VAL* 3.4 41.4 + - + +
87V VAL* 5.1 1.6 - - + -
111V TRP* 4.0 26.0 - - + -
125V VAL* 3.4 11.5 + - - +
126V ASP 3.5 7.5 + - - -
127V ILE 3.2 0.4 - - - -
128V ASN* 1.3 76.5 - - - +
130V GLN* 1.3 65.3 + - - +
132V SER* 2.8 17.9 + - - -
133V PHE* 3.0 30.8 + - + -
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Residues in contact with GLN 130 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111V TRP* 2.8 35.9 + - + +
122V LEU* 4.9 8.1 - - + -
126V ASP 3.0 14.3 + - - +
127V ILE* 2.8 20.3 + - - +
129V THR* 1.3 71.5 - - - +
131V GLN* 1.3 54.3 + - - -
133V PHE* 3.0 10.8 + - - +
134V GLU* 2.9 45.2 + - - +
140V ALA 3.3 20.4 + - - -
141V VAL* 3.5 1.2 - - - +
142V ALA* 3.1 23.7 + - + +
161V ARG* 4.7 3.3 - - - +
162V LEU* 3.6 25.8 - - + +
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Residues in contact with GLN 131 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127V ILE* 2.9 21.4 + - + +
128V ASN* 3.0 22.5 + - - +
130V GLN* 1.3 72.7 - - - +
132V SER* 1.3 57.8 + - - +
133V PHE 2.9 4.7 - - - -
134V GLU* 2.5 31.5 + - + +
135V ALA* 3.1 13.5 + - - +
162V LEU* 3.7 20.5 - - + +
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Residues in contact with SER 132 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84V VAL* 4.1 22.5 - - - +
128V ASN 3.0 10.9 + - - -
129V THR* 2.8 19.6 + - - -
131V GLN* 1.3 72.3 - - - +
133V PHE* 1.3 69.2 + - - +
135V ALA* 4.4 5.0 - - - +
136V LEU* 4.2 19.6 + - - +
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Residues in contact with PHE 133 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56V LEU* 4.0 13.7 - - + -
87V VAL* 3.7 32.8 - - + -
92V GLN* 6.1 1.8 - - - -
108V VAL* 5.7 7.4 - - + -
110V GLY* 5.3 2.0 - - - -
111V TRP* 3.2 53.8 - + + -
129V THR* 3.0 22.5 + - + -
130V GLN* 3.3 15.9 - - - +
131V GLN 2.9 0.8 - - - -
132V SER* 1.3 88.5 - - - +
134V GLU* 1.3 58.9 + - - +
135V ALA 3.5 0.4 - - - -
136V LEU* 4.0 23.4 - - + +
137V SER 3.0 20.4 + - - +
140V ALA* 3.2 18.5 - - + +
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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