Contacts of the helix formed by residues 164 - 177 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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160B GLU* 2.7 37.5 + - - +
161B MET* 3.5 16.8 + - - -
162B ALA 3.9 0.8 - - - -
163B VAL* 1.3 74.0 - - - +
165B ASP* 1.3 65.3 + - - +
166B ARG 3.3 2.9 + - - -
167B ASN* 3.3 8.8 + - - +
168B LEU* 2.9 31.1 + - - +
188B VAL* 4.1 19.5 - - - -
192B VAL* 4.0 6.4 - - - +
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Residues in contact with ASP 165 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172A HIS* 2.9 47.2 + - - +
175A ARG* 3.2 47.8 + - - +
176A SER* 4.0 12.1 + - - +
162B ALA 5.5 1.2 - - - +
163B VAL* 3.4 7.2 + - - -
164B SER* 1.3 77.1 + - - +
166B ARG* 1.3 58.0 + - - +
168B LEU* 3.2 7.7 + - - +
169B SER* 2.8 28.8 + - - -
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Residues in contact with ARG 166 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98A GLU* 2.7 43.8 + - - -
173A MET* 4.1 12.6 - - + -
176A SER* 3.6 23.9 - - - +
177A TYR* 5.1 2.9 - - - -
94B GLU* 2.7 46.6 + - - +
96B PHE* 4.1 3.6 - - - +
114B ASN* 3.7 12.7 - - - +
163B VAL 5.2 0.6 + - - +
164B SER* 3.3 1.0 - - - +
165B ASP* 1.3 77.2 - - - +
167B ASN* 1.3 61.8 + - - +
169B SER* 2.9 26.1 + - - -
170B LEU* 3.0 27.9 + - + +
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Residues in contact with ASN 167 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114B ASN* 3.1 36.1 + - - +
118B LEU* 3.6 7.7 - - + +
160B GLU* 4.3 16.0 + - - -
164B SER* 3.3 9.8 + - - +
166B ARG* 1.3 78.9 + - - +
168B LEU* 1.3 58.3 + - - +
170B LEU* 3.1 10.8 + - - +
171B ALA* 2.9 24.3 + - - +
188B VAL* 3.5 28.3 - - + +
191B TYR* 4.3 21.7 - - - -
192B VAL* 4.7 6.7 - - - +
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Residues in contact with LEU 168 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172A HIS* 3.8 30.5 - - + +
161B MET* 6.5 2.0 - - + -
164B SER* 2.9 28.5 + - - +
165B ASP* 3.5 7.4 - - - +
167B ASN* 1.3 76.4 - - - +
169B SER* 1.3 58.5 + - - +
171B ALA* 3.4 0.9 + - - +
172B HIS* 2.9 37.5 + - - +
184B ALA* 4.0 2.7 - - + +
185B GLU* 3.7 52.3 - - + +
188B VAL* 3.7 19.3 - - + -
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Residues in contact with SER 169 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169A SER* 2.6 50.2 + - - +
172A HIS* 3.8 7.6 - - - +
173A MET* 3.2 36.1 - - - +
165B ASP 2.8 13.0 + - - -
166B ARG 2.9 14.6 - - - -
168B LEU* 1.3 78.7 - - - +
170B LEU* 1.3 59.5 + - - +
172B HIS 3.4 0.2 + - - -
173B MET* 3.1 9.8 + - - -
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Residues in contact with LEU 170 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173A MET* 4.0 14.4 - - + -
94B GLU* 4.6 1.6 - - - +
96B PHE* 3.8 43.1 - - + -
114B ASN* 3.6 32.3 - - + -
115B ALA* 4.0 15.0 - - + +
118B LEU* 3.7 9.4 - - + -
166B ARG* 3.0 29.9 + - - +
167B ASN* 3.1 15.2 + - - +
169B SER* 1.3 76.6 - - - +
171B ALA* 1.3 56.0 + - - +
173B MET* 3.5 5.2 + - - +
174B LEU* 2.9 35.7 + - - +
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Residues in contact with ALA 171 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118B LEU* 3.9 4.7 - - + +
167B ASN 2.9 15.5 + - - +
168B LEU 3.6 2.2 - - - +
169B SER 3.3 0.2 - - - -
170B LEU* 1.3 74.0 - - - +
172B HIS* 1.3 59.8 + - - +
174B LEU* 3.2 8.0 + - - +
175B ARG* 2.8 30.7 + - - +
180B LEU* 3.8 18.2 - - + +
184B ALA* 3.6 27.1 - - + +
187B ILE* 5.2 0.2 - - + -
188B VAL* 3.6 16.6 - - + -
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Residues in contact with HIS 172 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165A ASP* 2.9 45.6 + - - +
168A LEU* 3.7 27.9 - - + +
169A SER* 3.8 9.4 - - - +
172A HIS* 3.3 28.4 + + - -
168B LEU* 2.9 26.2 + - + +
170B LEU 3.4 0.2 - - - -
171B ALA* 1.3 72.6 - - - +
173B MET* 1.3 67.9 + - - +
175B ARG* 3.0 7.3 + - - +
176B SER* 2.9 19.4 + - - -
184B ALA* 3.6 19.5 - - + +
185B GLU* 3.3 25.4 + - - -
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Residues in contact with MET 173 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96A PHE* 4.8 5.2 - - + -
166A ARG* 4.1 15.9 - - + -
169A SER* 3.1 37.6 + - - +
170A LEU* 4.4 13.9 - - + -
96B PHE* 3.8 35.7 - - + -
98B GLU* 3.7 28.3 - - + +
101B LEU* 4.0 7.6 - - + -
169B SER 3.1 8.4 + - - +
170B LEU* 3.7 5.2 - - - +
172B HIS* 1.3 78.3 - - - +
174B LEU* 1.3 64.5 + - - +
176B SER* 2.5 27.8 + - - -
177B TYR* 3.2 31.8 + - - -
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Residues in contact with LEU 174 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96B PHE* 5.7 2.0 - - + -
101B LEU* 4.2 18.2 - - + -
108B PRO* 4.1 17.5 - - + -
115B ALA* 3.5 33.9 - - + +
118B LEU* 3.9 19.1 - - + -
119B ALA 4.4 1.1 - - - +
170B LEU 2.9 28.0 + - - +
171B ALA* 3.3 7.6 - - - +
173B MET* 1.3 77.9 - - + +
175B ARG* 1.3 61.0 + - - +
177B TYR* 3.0 9.4 + - - +
178B GLY 3.1 0.2 + - - -
179B VAL* 2.9 44.1 + - + +
180B LEU* 3.7 23.1 - - + -
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Residues in contact with ARG 175 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162A ALA 6.0 0.2 + - - -
165A ASP* 2.5 46.7 + - - +
171B ALA 2.8 18.4 + - - +
172B HIS* 3.3 9.0 - - - +
174B LEU* 1.3 71.4 - - - +
176B SER* 1.3 57.9 + - - +
178B GLY* 2.7 25.1 + - - -
180B LEU* 3.4 27.3 - - + +
181B GLN 3.3 17.8 + - - -
182B ASP 2.7 27.2 + - - +
183B SER* 4.1 3.7 - - - +
184B ALA* 3.8 20.0 - - - +
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Residues in contact with SER 176 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165A ASP* 3.9 8.2 - - - +
166A ARG* 3.9 27.6 - - - +
172B HIS 2.9 12.2 + - - -
173B MET* 2.5 26.1 + - - -
175B ARG* 1.3 75.2 - - - +
177B TYR* 1.3 73.7 + - - +
178B GLY 3.3 0.8 + - - -
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Residues in contact with TYR 177 (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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166A ARG* 4.8 3.5 + - - -
98B GLU* 2.6 32.4 + - + +
101B LEU* 3.4 56.1 - - + -
102B GLU* 3.8 18.1 + - + +
106B HIS* 4.0 29.9 - + + +
173B MET* 3.2 26.9 + - - +
174B LEU 3.0 7.2 + - - +
175B ARG 3.0 1.2 - - - -
176B SER* 1.3 104.9 + - - +
178B GLY* 1.3 62.0 + - - +
179B VAL* 3.4 10.5 + - + +
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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