Contacts of the helix formed by residues 146 - 155 (chain u) 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 146 (chain u).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12u LEU* 3.5 29.8 - - + -
142u GLY* 2.8 18.6 + - - +
145u LEU* 1.3 75.6 - - - +
147u GLN* 1.3 66.4 + - - +
148u PRO 3.3 0.2 - - - -
149u LEU* 3.1 11.0 + - - +
150u LEU* 3.0 23.9 + - - +
172u CYS* 3.7 24.6 - - + +
175u VAL* 5.5 0.9 - - - -
176u LEU* 4.6 7.9 - - + -
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Residues in contact with GLN 147 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36t HIS 4.7 7.1 + - - -
132u TYR* 5.7 1.4 + - - -
134u ALA* 5.6 0.2 - - - +
136u SER* 3.2 49.5 + - - -
137u LEU* 3.9 4.8 + - - +
138u ALA* 3.9 10.3 - - + +
142u GLY 2.8 14.7 + - - +
143u ALA* 3.8 15.9 - - + +
146u ALA* 1.3 78.4 - - - +
148u PRO* 1.3 62.0 - - + +
150u LEU* 3.8 10.0 - - - +
151u ARG* 2.9 68.4 + - - +
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Residues in contact with PRO 148 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133b ALA* 3.9 25.1 - - + +
137b VAL* 6.4 0.2 - - - -
161b ALA* 4.6 8.1 - - + +
165b ASN* 3.7 39.6 + - + +
143u ALA 4.3 2.9 - - - +
144u TYR* 3.6 20.4 - - - +
145u LEU 3.6 13.2 - - - +
146u ALA 3.5 3.4 - - - -
147u GLN* 1.3 94.2 - - + +
149u LEU* 1.3 60.5 + - + +
151u ARG* 3.9 1.7 - - + +
152u GLU* 3.0 29.9 + - - +
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Residues in contact with LEU 149 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136b ALA* 3.9 20.9 - - + +
137b VAL* 4.2 31.6 - - + +
140b ASP* 4.6 17.3 - - + +
141b LYS* 5.4 3.4 - - - -
145u LEU 4.1 4.7 - - - +
146u ALA 3.1 6.4 + - - +
148u PRO* 1.3 77.8 - - + +
150u LEU* 1.3 67.6 + - - +
152u GLU* 3.1 19.9 + - - +
153u VAL* 3.0 28.8 + - - +
168u LEU* 4.8 1.6 - - + -
171u ARG* 4.9 13.0 + - + +
172u CYS* 4.1 17.7 - - - +
175u VAL* 3.7 28.9 - - + -
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Residues in contact with LEU 150 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12u LEU* 4.1 27.6 - - + -
13u GLY 4.6 4.0 - - - +
14u VAL* 4.7 15.7 - - + -
136u SER* 4.0 18.8 - - - -
137u LEU 4.5 4.9 - - - +
146u ALA 3.0 15.8 + - - +
147u GLN* 3.8 18.4 - - - +
149u LEU* 1.3 78.2 - - - +
151u ARG* 1.3 57.8 + - - +
153u VAL* 3.3 2.4 + - - +
154u LEU* 3.0 34.4 + - + +
168u LEU* 3.7 38.8 - - + +
169u VAL* 5.3 3.1 - - + +
172u CYS* 3.7 11.0 - - + -
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Residues in contact with ARG 151 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165b ASN* 2.2 38.5 + - - +
35t ILE* 2.3 48.9 + - - +
36t HIS 4.1 4.0 + - - -
37t THR* 5.7 1.2 - - - +
38t ARG* 4.1 24.5 - - - +
135u PRO* 6.4 0.9 - - + -
136u SER* 3.9 15.7 - - - +
143u ALA 5.6 0.8 + - - -
147u GLN* 2.9 54.0 + - - +
148u PRO* 4.0 3.3 - - + +
150u LEU* 1.3 75.2 - - - +
152u GLU* 1.3 67.4 + - - +
154u LEU* 4.4 4.3 - - - +
155u GLU* 3.0 45.5 + - - +
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Residues in contact with GLU 152 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137b VAL* 5.2 6.6 - - - +
141b LYS* 3.5 15.1 + - - -
157b GLU* 3.3 30.9 - - - +
161b ALA* 6.5 0.4 - - - -
148u PRO 3.0 19.4 + - - +
149u LEU* 3.1 23.1 + - - +
151u ARG* 1.3 77.9 - - - +
153u VAL* 1.3 65.7 + - - +
155u GLU* 3.7 4.3 + - - +
156u LYS* 3.6 18.4 + - - +
171u ARG* 5.6 1.9 + - - -
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Residues in contact with VAL 153 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149u LEU 3.0 17.1 + - - +
150u LEU 3.6 6.5 - - - +
152u GLU* 1.3 80.8 - - + +
154u LEU* 1.3 60.6 + - - +
155u GLU 3.1 0.4 - - - -
156u LYS* 2.9 20.8 + - - +
157u GLN* 2.9 16.4 + - + +
160u LEU* 4.0 24.5 - - + -
168u LEU* 3.8 35.7 - - + -
171u ARG* 4.7 14.8 - - - +
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Residues in contact with LEU 154 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14u VAL* 4.0 11.9 - - + -
15u LYS* 4.9 4.5 - - + +
135u PRO* 3.6 40.8 - - + +
136u SER* 3.6 22.0 - - - +
150u LEU* 3.0 17.3 + - + +
151u ARG* 4.1 4.3 - - - +
153u VAL* 1.3 82.0 - - + +
155u GLU* 1.3 60.9 + - + +
156u LYS 3.4 0.7 - - - -
157u GLN 4.0 4.7 - - - +
158u PRO* 3.3 46.6 - - + +
160u LEU* 3.7 29.8 - - + -
168u LEU* 5.1 1.3 - - + -
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Residues in contact with GLU 155 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38t ARG* 3.7 28.5 + - - +
212t LYS* 6.2 0.2 - - - +
151u ARG* 3.0 37.0 + - - +
152u GLU* 4.0 5.6 - - - +
153u VAL 3.1 0.2 - - - -
154u LEU* 1.3 80.3 - - + +
156u LYS* 1.3 58.0 + - - +
158u PRO* 5.2 3.8 - - - -
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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