Contacts of the strand formed by residues 158 - 163 (chain B) in PDB entry 5IH2
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 ILE 158 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160A ARG* 4.6 5.1 - - - +
179A ARG* 5.4 1.2 + - - -
201A PEG 5.9 5.4 - - - +
136B TYR* 3.9 30.3 - - + -
137B VAL 3.3 5.8 - - - +
138B ARG* 3.3 54.1 - - + +
156B GLY 3.5 5.1 + - - +
157B ASP* 1.3 74.9 - - - +
159B LEU* 1.3 68.2 + - - +
173B GLU 4.5 0.5 - - - +
175B SER* 4.6 5.0 + - - -
201B P4G 3.8 34.0 - - - +
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Residues in contact with LEU 159 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136B TYR* 3.2 6.5 - - - -
137B VAL* 2.8 48.9 + - + +
139B ALA* 5.1 1.1 - - + +
151B LEU* 4.0 8.7 - - + -
153B PHE* 3.6 42.0 - - + -
157B ASP* 4.3 19.5 - - + +
158B ILE* 1.3 83.9 - - - +
160B ARG* 1.3 62.0 + - - +
161B ILE 3.8 0.2 + - - -
172B ALA* 4.2 9.4 - - + -
173B GLU 3.5 4.9 - - - +
174B ASP* 3.9 27.6 - - + -
182B ILE* 4.1 20.6 - - + -
187B VAL* 4.7 2.9 - - + -
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Residues in contact with ARG 160 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134B ALA* 3.8 24.9 - - + +
135B GLU 3.4 11.7 - - - +
136B TYR* 3.7 24.8 - - + -
158B ILE 4.4 0.2 - - - -
159B LEU* 1.3 73.2 - - - +
161B ILE* 1.3 77.3 + - - +
162B ARG* 3.6 23.7 + - - +
172B ALA* 3.1 5.2 - - - -
173B GLU* 2.9 59.5 + - + +
179B ARG* 5.8 1.2 - - - +
201B P4G 3.9 23.2 - - - +
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Residues in contact with ILE 161 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135B GLU* 2.7 42.5 + - + +
137B VAL* 3.8 40.4 - - + -
159B LEU 4.5 0.2 - - - +
160B ARG* 1.3 84.4 + - - +
162B ARG* 1.3 64.1 + - - +
163B ASP 4.0 13.0 - - - +
164B LYS* 4.0 17.3 - - + -
170B TRP* 3.8 28.3 - - + -
171B ASN 3.8 6.3 - - - +
172B ALA* 4.0 7.6 - - + -
182B ILE* 3.8 19.7 - - + -
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Residues in contact with ARG 162 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160B ARG* 4.1 28.8 - - - +
161B ILE* 1.3 77.5 - - - +
163B ASP* 1.3 64.4 + - + +
171B ASN* 2.7 55.1 + - - +
172B ALA* 4.4 1.8 - - - -
173B GLU* 3.9 22.6 + - + -
179B ARG* 3.3 52.5 - - - +
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Residues in contact with ASP 163 (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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161B ILE* 3.8 1.4 - - - +
162B ARG* 1.3 86.6 - - + +
164B LYS* 1.3 70.7 + - - +
165B PRO* 3.3 18.3 - - + +
170B TRP* 3.4 6.9 - - - +
171B ASN* 2.8 42.6 + - + +
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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
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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