Contacts of the helix formed by residues 164 - 177 (chain A) in PDB entry 3IH9
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 164 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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160A GLU* 2.6 31.9 + - - +
161A MET* 3.2 25.2 + - - -
162A ALA 3.8 0.4 - - - -
163A VAL* 1.3 72.9 - - - +
165A ASP* 1.3 64.9 + - - +
166A ARG 3.3 3.7 + - - -
167A ASN* 3.3 11.0 + - - +
168A LEU* 2.9 33.9 + - - +
188A VAL* 4.0 20.2 - - - -
192A VAL* 4.3 0.9 - - - +
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Residues in contact with ASP 165 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162A ALA 5.3 1.2 - - - +
163A VAL* 3.3 8.7 - - - -
164A SER* 1.3 78.9 + - - +
166A ARG* 1.3 58.7 + - - +
168A LEU* 3.3 4.3 + - - +
169A SER* 2.9 24.8 + - - -
172B HIS* 2.9 54.1 + - - +
175B ARG* 2.5 45.9 + - - +
176B SER* 3.9 12.8 + - - +
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Residues in contact with ARG 166 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94A GLU* 2.8 50.5 + - - +
95A ALA* 4.4 0.2 - - - +
96A PHE* 4.2 1.8 - - - +
114A ASN* 3.4 20.2 - - - +
163A VAL 5.0 1.6 + - - +
164A SER 3.3 0.8 - - - -
165A ASP* 1.3 78.0 - - - +
167A ASN* 1.3 63.0 + - - +
169A SER* 2.9 26.2 + - - -
170A LEU* 3.0 21.5 + - + +
98B GLU* 2.8 43.5 + - - -
173B MET* 4.1 13.0 - - + -
176B SER* 3.9 20.0 - - - -
177B TYR* 5.2 2.9 - - - -
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Residues in contact with ASN 167 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114A ASN* 3.2 33.7 + - - +
118A LEU* 3.8 8.1 - - + +
160A GLU* 4.3 16.2 + - - -
164A SER* 3.3 9.6 + - - +
166A ARG* 1.3 80.1 + - - +
168A LEU* 1.3 56.7 + - - +
170A LEU* 3.1 10.6 + - - +
171A ALA* 2.8 30.8 + - - +
188A VAL* 3.6 23.2 - - + +
191A TYR* 4.3 20.7 - - - -
192A VAL* 4.7 7.9 - - - +
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Residues in contact with LEU 168 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161A MET* 5.8 1.8 - - + +
164A SER* 2.9 35.2 + - - +
165A ASP* 3.5 7.4 - - - +
167A ASN* 1.3 76.2 - - - +
169A SER* 1.3 56.3 + - - +
171A ALA* 3.8 1.1 - - - +
172A HIS* 2.8 41.7 + - + +
184A ALA* 3.9 7.4 - - + +
185A GLU* 3.9 27.1 - - + +
188A VAL* 3.8 24.0 - - + -
172B HIS* 3.7 32.5 - - + +
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Residues in contact with SER 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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165A ASP 2.9 13.0 + - - -
166A ARG 2.9 14.8 - - - -
168A LEU* 1.3 77.1 - - - +
170A LEU* 1.3 60.7 + - - +
173A MET* 3.0 9.0 + - - +
96B PHE* 5.7 0.3 - - - -
169B SER* 2.6 50.2 + - - +
172B HIS* 3.8 8.0 - - - +
173B MET* 3.1 35.8 - - - +
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Residues in contact with LEU 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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94A GLU* 4.2 2.2 - - - +
96A PHE* 3.7 46.2 - - + -
114A ASN* 3.5 32.8 - - + -
115A ALA* 3.8 16.8 - - + +
118A LEU* 3.7 9.0 - - + -
166A ARG* 3.0 32.7 + - - +
167A ASN* 3.1 14.8 + - - +
169A SER* 1.3 75.9 - - - +
171A ALA* 1.3 58.8 + - - +
173A MET* 3.1 6.4 + - - +
174A LEU* 2.9 34.0 + - - +
173B MET* 4.4 9.4 - - + -
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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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118A LEU* 4.0 7.5 - - + +
167A ASN 2.8 19.1 + - - +
168A LEU 3.8 0.4 - - - +
170A LEU* 1.3 71.9 - - - +
172A HIS* 1.3 57.6 + - - +
174A LEU* 3.3 8.1 + - - +
175A ARG* 2.9 26.9 + - - +
180A LEU* 3.5 28.3 - - + +
184A ALA* 3.7 17.3 - - + +
187A ILE* 5.1 0.2 - - + -
188A VAL* 3.7 21.1 - - + -
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Residues in contact with HIS 172 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168A LEU* 2.8 29.5 + - + +
171A ALA* 1.3 75.4 - - - +
173A MET* 1.3 64.3 + - - +
175A ARG* 3.1 3.1 + - - +
176A SER* 2.9 18.5 + - - -
184A ALA* 3.4 23.2 - - + +
165B ASP* 2.9 50.1 + - - +
168B LEU* 3.8 25.4 - - + +
169B SER* 3.8 9.4 - - - -
172B HIS* 3.3 34.4 + + - -
185B GLU* 4.2 6.7 + - - -
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Residues in contact with MET 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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96A PHE* 3.8 34.8 - - + -
98A GLU* 3.8 26.2 - - + +
101A LEU* 4.0 8.5 - - + -
169A SER 3.0 7.9 + - - +
170A LEU* 3.5 8.7 - - - +
172A HIS* 1.3 75.4 - - - +
174A LEU* 1.3 61.6 + - + +
176A SER* 2.9 25.7 - - - -
177A TYR* 3.2 32.5 + - + -
96B PHE* 4.8 5.6 - - + -
166B ARG* 4.1 16.6 - - + -
169B SER* 3.2 40.0 + - - +
170B LEU* 4.0 18.8 - - + -
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Residues in contact with LEU 174 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96A PHE* 5.4 2.2 - - + -
101A LEU* 3.9 23.6 - - + -
108A PRO* 4.1 15.9 - - + -
115A ALA* 3.4 36.3 - - + +
118A LEU* 4.0 18.2 - - + -
119A ALA 4.5 3.4 - - - +
170A LEU 2.9 24.7 + - - +
171A ALA* 3.5 6.7 - - - +
172A HIS 3.2 0.2 - - - -
173A MET* 1.3 75.3 - - + +
175A ARG* 1.3 62.5 + - - +
177A TYR* 3.3 1.9 + - - -
178A GLY 3.2 3.5 + - - -
179A VAL* 2.8 49.6 + - + +
180A LEU* 3.9 16.6 - - + -
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Residues in contact with ARG 175 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171A ALA 2.9 10.2 + - - +
172A HIS* 3.5 8.2 - - - +
174A LEU* 1.3 73.4 - - - +
176A SER* 1.3 60.0 + - - +
178A GLY* 2.8 23.2 + - - -
180A LEU* 3.6 25.5 + - + +
181A GLN* 2.7 30.5 + - - +
182A ASP 3.0 24.5 + - - +
183A SER* 4.2 4.4 - - - +
184A ALA* 3.6 23.9 - - - +
162B ALA 5.9 1.2 + - - -
165B ASP* 3.2 35.8 + - - +
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Residues in contact with SER 176 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172A HIS 2.9 12.7 + - - -
173A MET* 2.9 20.2 - - - -
175A ARG* 1.3 79.1 - - - +
177A TYR* 1.3 68.0 + - - +
178A GLY 3.5 0.5 + - - -
165B ASP* 4.0 7.8 - - - +
166B ARG* 3.6 33.7 + - - +
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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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98A GLU* 2.5 34.2 + - + +
101A LEU* 3.5 43.3 - - + -
102A GLU* 3.3 18.6 + - + +
106A HIS* 3.5 41.5 + + + +
173A MET* 3.2 38.0 + - - +
174A LEU 3.3 4.5 + - - +
175A ARG 3.2 0.4 - - - -
176A SER* 1.3 84.3 - - - +
178A GLY* 1.3 62.4 + - - +
179A VAL* 3.3 11.0 + - + +
166B ARG* 4.6 3.7 + - - -
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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