Contacts of the helix formed by residues 164 - 181 (chain A) in PDB entry 1G5J
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 GLN 164 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30A GLN* 5.6 2.0 + - - +
31A PHE* 4.0 23.5 - - + +
159A VAL* 3.1 35.9 - - + +
162A GLU* 4.3 12.8 - - - +
163A MET* 1.3 73.1 - - - +
165A VAL* 1.3 57.9 + - - +
166A LEU 2.9 5.6 - - - -
167A VAL* 2.6 33.5 + - - +
168A SER* 3.9 2.8 + - - -
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Residues in contact with VAL 165 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120A PRO* 4.1 35.2 - - + -
163A MET* 3.5 1.7 - - - -
164A GLN* 1.3 80.4 + - - +
166A LEU* 1.3 58.5 + - + +
168A SER* 4.4 2.0 + - - -
169A ARG* 3.1 40.8 + - + +
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Residues in contact with LEU 166 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118A ILE* 4.2 11.2 - - + -
119A THR* 4.2 1.8 - - - -
120A PRO* 3.6 39.7 - - + -
121A GLY 4.4 2.5 - - - +
123A ALA* 3.5 29.8 - - + -
158A SER* 4.3 12.8 - - - -
163A MET* 3.6 33.7 - - + +
164A GLN 2.8 0.8 + - - -
165A VAL* 1.3 82.7 - - + +
167A VAL* 1.3 69.1 + - - +
169A ARG* 4.1 9.4 - - - -
170A ILE* 2.8 43.0 + - + +
173A TRP* 5.0 1.3 - - + -
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Residues in contact with VAL 167 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A LEU* 4.6 1.9 - - - +
28A TRP* 3.4 35.4 - - + -
31A PHE* 4.1 17.9 - - + -
155A CYS* 3.7 27.9 - - + +
158A SER* 5.1 0.8 + - - +
159A VAL* 3.3 36.3 - - + -
163A MET 4.5 1.8 - - - +
164A GLN* 2.6 23.8 + - + +
166A LEU* 1.3 76.8 - - - +
168A SER* 1.3 65.0 + - - +
170A ILE* 2.8 11.8 + - - +
171A ALA* 3.0 11.1 + - - +
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Residues in contact with SER 168 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A ARG* 4.9 1.4 + - - -
28A TRP* 5.5 1.1 - - - -
31A PHE* 4.9 9.9 - - - -
32A SER* 4.2 19.0 + - - -
164A GLN 3.9 2.7 + - - -
165A VAL 5.1 1.8 - - - -
167A VAL* 1.3 83.4 - - - +
169A ARG* 1.3 66.3 + - - +
171A ALA* 3.0 18.6 + - - +
172A ALA* 3.0 15.8 + - - +
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Residues in contact with ARG 169 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120A PRO 5.3 0.2 - - - -
121A GLY* 4.4 22.8 - - - +
124A TYR* 6.0 2.2 - - - +
165A VAL* 3.1 38.0 + - + +
166A LEU* 3.7 8.5 - - - +
168A SER* 1.3 81.2 + - - +
170A ILE* 1.3 53.7 + - - +
172A ALA* 3.8 4.1 + - - +
173A TRP* 2.7 71.5 + - + +
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Residues in contact with ILE 170 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A LEU* 5.2 2.2 - - + -
118A ILE* 6.1 2.0 - - + -
123A ALA* 5.5 3.6 - - + -
127A PHE* 3.6 19.5 - - + -
151A GLY* 4.2 12.6 - - - +
154A LEU* 4.5 22.4 - - + -
155A CYS* 4.9 8.7 - - + -
158A SER* 4.7 7.6 - - - +
166A LEU* 2.8 38.0 + - + +
167A VAL 3.3 3.6 - - - +
169A ARG* 1.3 75.6 - - - +
171A ALA* 1.3 67.5 + - - +
173A TRP* 3.0 28.0 + - + +
174A MET* 2.9 41.9 + - - +
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Residues in contact with ALA 171 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A ARG* 4.2 5.4 - - - +
13A VAL* 3.3 22.7 - - + +
14A VAL* 5.0 4.5 - - + -
17A LEU* 3.0 33.2 - - + +
28A TRP* 4.5 6.3 - - + -
32A SER* 6.1 0.7 - - - +
167A VAL 3.0 8.9 + - - +
168A SER* 3.0 13.4 + - - +
170A ILE* 1.3 77.4 - - - +
172A ALA* 1.3 62.2 + - - +
174A MET* 3.3 5.4 + - - +
175A ALA 3.2 16.5 + - - -
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Residues in contact with ALA 172 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A ARG* 3.3 27.1 - - - +
168A SER* 3.0 14.2 + - - +
169A ARG* 4.0 5.2 - - - +
171A ALA* 1.3 77.5 - - - +
173A TRP* 1.3 61.4 + - + +
175A ALA* 3.2 3.0 + - - +
176A THR* 2.5 42.5 + - - +
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Residues in contact with TRP 173 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123A ALA* 4.1 23.6 - - + -
124A TYR* 4.1 24.0 - - + -
127A PHE* 3.7 37.5 - + + -
166A LEU* 5.0 1.1 - - + -
169A ARG* 2.7 64.4 + - + +
170A ILE* 3.0 32.2 + - + +
172A ALA* 1.3 83.3 - - + +
174A MET* 1.3 57.0 + - - +
176A THR* 4.3 4.0 - - - -
177A TYR* 3.0 33.4 + - - +
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Residues in contact with MET 174 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13A VAL* 4.0 22.4 - - + +
17A LEU* 4.1 15.3 - - + +
127A PHE* 3.5 17.7 - - + -
147A PHE* 3.3 36.8 - - + +
148A PHE* 3.3 44.0 - - + +
151A GLY* 3.9 9.6 - - - -
170A ILE* 2.9 38.2 + - - +
171A ALA* 3.6 11.0 - - - +
172A ALA 3.2 0.2 - - - -
173A TRP* 1.3 75.6 - - - +
175A ALA* 1.3 61.7 + - - +
177A TYR* 3.4 6.6 - - - +
178A LEU* 3.8 8.5 - - - +
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Residues in contact with ALA 175 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6A SER* 5.3 7.7 - - - +
9A ASN* 4.1 2.9 + - + +
10A ARG* 4.0 23.1 - - + +
13A VAL* 3.6 30.2 - - + +
171A ALA 3.2 4.7 + - - +
172A ALA* 3.8 5.8 - - - +
174A MET* 1.3 75.2 - - - +
176A THR* 1.3 60.8 + - - +
177A TYR 3.0 1.8 - - - -
178A LEU* 2.8 41.7 + - + +
179A ASN* 3.6 3.2 + - - +
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Residues in contact with THR 176 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6A SER* 6.1 0.7 - - - -
172A ALA* 2.5 31.8 + - - +
173A TRP* 4.3 4.2 - - - -
175A ALA* 1.3 74.0 - - - +
177A TYR* 1.3 55.2 + - - +
178A LEU 2.9 0.3 + - - -
179A ASN* 3.0 30.6 + - - +
180A ASP* 2.6 49.7 + - + +
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Residues in contact with TYR 177 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127A PHE* 5.1 3.8 - + - -
128A GLU* 5.1 1.8 - - - -
131A VAL* 3.1 56.7 + - + +
132A ASN* 5.1 1.2 + - - -
135A PHE* 4.1 14.3 - + - +
147A PHE* 4.0 14.1 - + + -
173A TRP 3.0 19.9 + - - +
174A MET 3.4 11.0 - - - +
175A ALA 3.0 0.6 + - - -
176A THR* 1.3 76.7 - - - +
178A LEU* 1.3 50.2 + - + +
180A ASP* 4.6 0.2 - - - -
181A HIS* 2.6 61.7 + + + +
182A LEU* 2.6 53.7 + - + -
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Residues in contact with LEU 178 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5A MET* 5.0 0.2 - - + -
9A ASN* 3.0 44.9 - - + +
144A ILE* 4.5 8.7 - - + -
147A PHE* 5.5 2.9 - - + -
148A PHE* 4.7 11.4 - - + -
174A MET 3.8 8.5 - - - +
175A ALA* 2.8 26.9 + - - +
177A TYR* 1.3 74.7 - - + +
179A ASN* 1.3 56.3 - - - +
180A ASP 3.0 2.4 + - - -
182A LEU* 2.6 50.3 + - + +
183A GLU* 2.8 19.3 + - - +
186A ILE* 3.8 12.6 - - + -
192A TRP* 3.5 25.8 - - + -
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Residues in contact with ASN 179 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3A MET* 3.9 23.8 - - + +
5A MET* 3.3 22.8 - - + +
6A SER* 4.4 8.6 - - - -
175A ALA 3.6 2.0 + - - -
176A THR* 3.0 38.3 + - - +
178A LEU* 1.3 79.8 - - - +
180A ASP* 1.3 65.2 + - - +
183A GLU* 3.4 19.1 - - - +
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Residues in contact with ASP 180 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176A THR* 2.6 32.0 + - + +
177A TYR* 4.6 0.2 - - - -
178A LEU 4.0 0.4 - - - -
179A ASN* 1.3 87.5 + - - +
181A HIS* 1.3 81.4 + - + +
183A GLU* 5.0 1.7 - - - +
184A PRO* 5.4 1.4 - - - +
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Residues in contact with HIS 181 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128A GLU* 5.2 5.6 + - - -
177A TYR* 2.6 63.7 + + + +
180A ASP* 1.3 88.9 + - + +
182A LEU* 1.3 59.3 + - + +
183A GLU 2.6 17.3 + - - -
184A PRO* 3.5 15.6 - - - +
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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
------------------------------------------------------------
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