Contacts of the helix formed by residues 162 - 173 (chain F) in PDB entry 5GAH
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 162 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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124F GLY 4.3 5.6 - - - -
125F ARG 4.1 3.6 - - - -
126F GLY* 3.6 11.0 - - - -
160F ALA* 3.4 4.0 - - - +
161F LYS* 1.3 79.8 - - - +
163F ASP* 1.3 65.4 + - - +
164F GLU* 2.9 26.2 + - - +
165F GLU* 3.4 15.3 + - - +
166F GLY 3.4 14.9 + - - -
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Residues in contact with ASP 163 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122F PHE* 3.3 30.4 - - + +
124F GLY* 3.0 31.1 + - - -
126F GLY* 2.9 28.9 + - - -
162F SER* 1.3 71.8 + - - +
164F GLU* 1.3 60.1 + - - +
166F GLY 3.4 1.0 + - - -
167F ARG* 2.9 46.3 + - - +
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Residues in contact with GLU 164 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20F PHE* 4.0 21.3 - - + -
162F SER* 2.9 13.4 + - - +
163F ASP* 1.3 78.8 - - - +
165F GLU* 1.3 66.3 + - + +
167F ARG* 3.1 16.2 + - - +
168F ALA* 3.0 23.0 + - - +
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Residues in contact with GLU 165 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16F LEU* 4.8 0.2 - - - +
20F PHE* 3.4 23.6 - - + -
22F TYR* 3.9 28.5 + - - +
27F GLN 5.5 0.5 - - - +
29F PRO* 4.0 7.2 - - + +
160F ALA* 3.5 14.7 - - + -
161F LYS* 3.0 39.8 + - - +
162F SER* 3.4 21.4 + - - +
163F ASP 3.4 0.2 - - - -
164F GLU* 1.3 75.9 - - + +
166F GLY* 1.3 58.2 + - - +
168F ALA* 3.5 2.1 + - - +
169F LEU* 2.9 30.2 + - - +
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Residues in contact with GLY 166 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122F PHE* 4.1 9.6 - - - -
126F GLY 4.3 10.8 - - - -
158F THR* 4.9 4.7 - - - -
160F ALA* 3.8 12.9 - - - +
162F SER 3.4 6.9 + - - -
163F ASP 3.4 5.3 + - - -
164F GLU 3.3 0.4 - - - -
165F GLU* 1.3 78.6 - - - +
167F ARG* 1.3 57.0 + - - +
169F LEU* 3.7 5.8 - - - +
170F LEU* 2.9 35.7 + - - +
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Residues in contact with ARG 167 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119F ALA* 2.7 47.2 + - - +
120F LYS* 5.0 0.2 - - - +
122F PHE* 4.0 19.4 - - + -
163F ASP* 2.9 36.9 + - - +
164F GLU* 3.5 11.5 + - - +
166F GLY* 1.3 74.5 - - - +
168F ALA* 1.3 61.0 + - - +
170F LEU* 4.0 2.2 - - - +
171F ALA* 2.9 35.2 + - + +
177F PHE* 4.1 12.0 - - + -
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Residues in contact with ALA 168 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15F LYS* 5.8 0.2 - - - -
16F LEU* 3.8 4.3 - - + +
19F GLU* 3.4 34.8 - - - +
20F PHE* 3.8 14.8 - - + -
164F GLU 3.0 15.6 + - - +
167F ARG* 1.3 78.4 - - - +
169F LEU* 1.3 57.1 + - - +
171F ALA* 3.6 6.0 + - - +
172F ALA* 2.9 28.8 + - - +
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Residues in contact with LEU 169 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8F TYR* 4.2 5.6 - - + -
12F VAL* 3.9 16.4 - - + -
16F LEU* 3.8 17.4 - - + +
29F PRO* 3.4 31.9 - - + +
31F VAL* 4.1 17.5 - - + -
158F THR* 3.8 28.5 - - + +
165F GLU 2.9 18.8 + - - +
166F GLY 3.7 3.8 - - - +
167F ARG 3.2 0.2 - - - -
168F ALA* 1.3 73.0 - - - +
170F LEU* 1.3 72.0 + - + +
172F ALA* 2.9 18.7 + - - +
173F PHE* 3.5 26.4 + - + -
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Residues in contact with LEU 170 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31F VAL* 5.9 3.6 - - + -
100F PHE* 3.7 30.3 - - + -
122F PHE* 3.9 16.4 - - + -
128F TYR* 3.7 34.5 - - + -
156F ILE* 4.2 17.0 - - + -
158F THR* 6.0 3.1 - - - +
166F GLY* 2.9 18.4 + - - +
167F ARG 4.0 2.7 - - - +
169F LEU* 1.3 77.5 - - + +
171F ALA* 1.3 63.7 + - - +
173F PHE* 3.1 17.8 + - + +
175F PHE* 3.1 44.3 + - + +
177F PHE* 4.2 4.7 - - + -
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Residues in contact with ALA 171 (chain F).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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167F ARG* 2.9 22.9 + - + +
168F ALA* 3.8 6.3 - - - +
170F LEU* 1.3 77.0 - - - +
172F ALA* 1.3 53.8 + - - +
173F PHE 3.1 0.4 - - - -
174F ASP* 2.7 26.7 + - - +
175F PHE 4.1 11.7 - - - +
177F PHE* 4.4 12.5 - - + -
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Residues in contact with ALA 172 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7F TYR* 3.0 27.4 + - - -
12F VAL* 3.5 28.4 - - + +
15F LYS* 4.4 22.8 - - + +
16F LEU* 4.2 7.4 - - + -
168F ALA 2.9 15.8 + - - +
169F LEU* 2.9 14.6 + - - +
171F ALA* 1.3 76.2 - - - +
173F PHE* 1.3 57.9 + - - +
174F ASP 3.2 1.1 + - - -
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Residues in contact with PHE 173 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4F LEU* 3.4 49.5 - - + +
7F TYR* 3.9 17.9 - + - -
8F TYR* 3.6 29.6 - + + -
12F VAL* 4.6 2.7 - - + -
31F VAL* 4.3 12.3 - - + -
97F TRP* 3.7 20.4 - + - -
100F PHE* 3.9 13.5 - + + -
104F ILE* 3.8 23.7 - - + +
169F LEU* 3.5 34.3 + - + -
170F LEU* 3.1 12.6 + - + +
172F ALA* 1.3 77.7 - - - +
174F ASP* 1.3 68.2 + - - +
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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