Contacts of the helix formed by residues 130 - 142 (chain b) 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 GLY 130 (chain b).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1b THR 3.1 7.5 + - - -
2b THR* 3.4 29.6 - - - +
128b GLY 3.1 1.2 - - - -
129b SER* 1.3 78.0 + - - +
131b SER* 1.3 62.9 + - - +
132b LEU 3.3 3.8 + - - -
133b ALA* 3.5 15.9 + - - +
134b ALA 3.5 8.1 + - - -
162b GLY* 3.8 2.2 - - - -
166b ASP* 3.7 17.3 - - - -
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Residues in contact with SER 131 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2b THR* 4.7 0.7 - - - -
126b THR* 3.0 30.2 + - - -
127b MET* 3.4 24.8 + - - -
128b GLY 2.3 26.9 + - - -
129b SER 3.3 1.3 + - - -
130b GLY* 1.3 79.5 - - - +
132b LEU* 1.3 71.9 + - - +
134b ALA* 3.5 2.2 + - - -
135b MET* 2.9 23.7 + - - +
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Residues in contact with LEU 132 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25a TYR* 3.0 64.6 - - + +
129b SER 4.9 1.8 + - - +
130b GLY 3.3 1.0 - - - -
131b SER* 1.3 87.8 - - - +
133b ALA* 1.3 63.8 + - - +
135b MET* 3.5 1.5 - - - +
136b ALA* 3.0 19.9 + - - +
141u TYR* 4.2 20.4 - - + -
144u TYR* 3.5 23.1 - - + +
145u LEU* 3.4 29.3 - - + +
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Residues in contact with ALA 133 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130b GLY* 3.5 12.2 + - - +
132b LEU* 1.3 74.2 - - - +
134b ALA* 1.3 67.0 + - - +
136b ALA* 3.0 15.2 + - - +
137b VAL* 3.0 14.7 + - - +
161b ALA* 3.7 34.2 - - + +
162b GLY* 3.7 1.8 - - - +
165b ASN* 4.4 5.8 - - + -
144u TYR 3.5 9.3 + - - +
148u PRO* 3.9 19.9 - - + +
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Residues in contact with ALA 134 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2b THR* 4.2 10.5 - - + -
4b ALA* 4.7 3.4 - - + -
126b THR* 3.6 22.0 - - + -
130b GLY 3.5 8.2 + - - +
131b SER 3.5 4.2 + - - +
132b LEU 3.4 0.2 - - - -
133b ALA* 1.3 80.1 - - - +
135b MET* 1.3 56.9 + - - +
137b VAL* 3.0 4.7 + - - +
138b PHE* 2.9 30.7 + - - -
158b ALA* 3.5 36.0 - - + +
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Residues in contact with MET 135 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25a TYR* 3.2 28.7 - - + +
27a ALA 5.4 1.3 - - - +
124b TYR* 4.1 17.0 - - + +
125b VAL* 5.2 0.2 - - - -
126b THR* 3.4 29.5 - - + +
131b SER 2.9 17.9 + - - +
132b LEU* 3.5 7.4 - - - +
133b ALA 3.1 0.2 - - - -
134b ALA* 1.3 72.8 - - - +
136b ALA* 1.3 61.2 + - - +
138b PHE* 3.3 2.5 + - - +
139b GLU* 2.9 35.5 + - - +
145u LEU* 4.5 2.7 - - + -
179u ARG* 3.1 56.8 - - + +
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Residues in contact with ALA 136 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132b LEU 3.0 10.4 + - - +
133b ALA* 3.0 12.0 + - - +
135b MET* 1.3 77.1 - - - +
137b VAL* 1.3 66.2 + - - +
139b GLU* 3.2 2.6 + - - +
140b ASP* 3.0 24.8 + - - +
145u LEU* 3.1 28.3 - - + +
148u PRO* 5.0 1.1 - - + -
149u LEU* 3.9 20.2 - - + +
175u VAL* 4.0 17.7 - - + +
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Residues in contact with VAL 137 (chain b).
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 3.0 7.4 + - - +
134b ALA 3.0 8.8 + - - +
136b ALA* 1.3 77.6 - - - +
138b PHE* 1.3 63.3 + - - +
140b ASP* 3.3 1.6 + - - +
141b LYS* 3.0 33.6 + - + +
154b LEU* 3.9 19.7 - - + +
157b GLU* 4.1 12.6 - - + +
158b ALA* 3.8 26.7 - - + +
161b ALA* 3.7 30.3 - - + -
148u PRO* 5.9 0.2 - - + -
149u LEU* 4.2 18.8 - - + -
152u GLU* 5.2 7.2 - - - +
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Residues in contact with PHE 138 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4b ALA* 3.8 18.8 - - + -
5b GLY 3.9 12.6 - - - -
6b VAL* 4.7 2.9 - - + -
124b TYR* 3.5 39.0 - + + -
125b VAL 3.7 21.3 - - - -
126b THR* 3.9 20.9 - - + -
134b ALA 2.9 9.1 + - - -
135b MET* 3.7 6.3 - - - +
137b VAL* 1.3 77.8 - - - +
139b GLU* 1.3 59.6 + - - +
140b ASP 3.0 0.2 + - - -
142b PHE* 2.9 38.5 + - + +
154b LEU* 3.7 37.0 - - + -
155b VAL* 4.2 17.9 - - + -
158b ALA* 3.6 18.4 - - + -
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Residues in contact with GLU 139 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29a ARG* 2.8 34.7 + - - -
124b TYR* 3.2 22.2 + - - +
135b MET* 2.9 36.6 + - - +
136b ALA* 3.2 6.0 + - - +
138b PHE* 1.3 72.0 - - - +
140b ASP* 1.3 59.1 + - - +
142b PHE 4.9 0.4 - - - -
174u ARG* 5.5 3.1 - - - +
175u VAL* 4.7 12.5 - - + +
178u TYR* 2.9 45.8 - - + +
179u ARG* 3.1 25.7 + - + +
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Residues in contact with ASP 140 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136b ALA 3.0 15.8 + - - +
137b VAL 3.8 2.7 - - - +
138b PHE 3.0 0.2 - - - -
139b GLU* 1.3 80.8 - - - +
141b LYS* 1.3 74.9 + - + +
142b PHE 3.7 3.2 + - - +
149u LEU* 4.6 16.2 - - + +
171u ARG* 2.8 59.5 + - - +
174u ARG* 5.1 4.0 + - - -
175u VAL* 4.8 4.6 - - + +
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Residues in contact with LYS 141 (chain b).
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* 3.0 22.3 + - + +
138b PHE 3.8 0.7 - - - -
140b ASP* 1.3 99.2 - - - +
142b PHE* 1.3 61.1 + - - +
143b ARG* 3.9 4.3 + - - +
146b MET* 4.6 5.0 - - - +
150b GLU* 5.8 0.2 - - - +
154b LEU* 3.6 21.8 - - + +
157b GLU* 2.3 39.7 + - - +
149u LEU* 5.4 3.6 - - - -
152u GLU* 3.5 22.2 + - - -
171u ARG* 4.9 6.3 - - - +
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Residues in contact with PHE 142 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6b VAL* 3.7 32.5 - - + -
7b VAL 4.3 11.0 - - - -
123b PRO* 3.9 15.7 - - + -
124b TYR* 3.5 35.4 - + + -
138b PHE* 2.9 22.8 + - - +
139b GLU 4.9 0.5 - - - +
140b ASP 3.7 2.9 - - - +
141b LYS* 1.3 78.9 - - - +
143b ARG* 1.3 85.3 + - - +
144b PRO* 4.1 11.2 - - + -
146b MET* 4.2 2.2 - - + -
154b LEU* 3.9 15.0 - - + -
208u ASN* 5.7 3.5 + - - -
211u ILE* 4.0 20.6 - - + -
214u MET* 4.8 2.7 - - + -
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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