Contacts of the strand formed by residues 158 - 163 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136A TYR* 4.0 26.5 - - + -
137A VAL 3.3 7.9 - - - +
138A ARG* 3.6 23.1 - - + +
156A GLY 3.7 12.1 - - - +
157A ASP* 1.3 72.0 - - - +
159A LEU* 1.3 67.5 + - - +
174A ASP* 4.3 2.8 - - - +
175A SER* 4.4 3.5 + - - -
190A TYR* 3.6 39.5 - - + -
201A PEG 3.5 28.8 - - - +
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Residues in contact with LEU 159 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136A TYR* 3.3 7.3 - - - -
137A VAL* 2.8 47.0 + - + +
139A ALA* 5.2 0.7 - - + -
151A LEU* 4.2 8.1 - - + -
153A PHE* 3.8 35.4 - - + -
157A ASP* 4.3 21.1 - - + +
158A ILE* 1.3 80.1 - - - +
160A ARG* 1.3 60.2 + - - +
172A ALA* 4.2 8.3 - - + -
173A GLU 3.3 4.5 - - - +
174A ASP* 3.6 31.2 - - + -
182A ILE* 4.0 25.1 - - + -
187A VAL* 4.6 5.6 - - + -
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Residues in contact with ARG 160 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134A ALA* 3.9 15.5 - - + +
135A GLU 3.6 8.5 - - - +
136A TYR* 3.6 38.5 - - + -
159A LEU* 1.3 72.1 - - - +
161A ILE* 1.3 79.6 + - - +
162A ARG* 3.5 11.3 + - - +
172A ALA* 3.2 3.3 - - - -
173A GLU* 2.8 64.1 + - + +
201A PEG 3.8 20.9 - - - -
155B LYS 4.2 4.2 + - - -
156B GLY* 3.6 29.6 + - - -
157B ASP* 2.9 35.2 + - - +
158B ILE* 4.6 3.8 - - - +
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Residues in contact with ILE 161 (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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135A GLU* 2.8 44.4 + - + +
137A VAL* 3.8 37.7 - - + -
160A ARG* 1.3 84.4 + - - +
162A ARG* 1.3 62.7 + - - +
163A ASP 4.0 14.6 - - - +
164A LYS* 4.1 14.8 - - + -
170A TRP* 3.8 34.3 - - + -
171A ASN 3.8 6.5 - - - +
172A ALA* 4.0 6.3 - - + -
182A ILE* 4.0 15.3 - - + -
155B LYS 5.1 2.1 - - - +
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Residues in contact with ARG 162 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160A ARG* 3.9 24.9 - - - +
161A ILE* 1.3 78.1 - - - +
163A ASP* 1.3 59.9 + - - +
171A ASN* 2.8 48.8 + - + +
173A GLU* 3.6 24.7 - - + -
179A ARG* 3.3 31.3 - - - +
142B ASP* 5.0 1.4 - - - +
152B PRO 5.2 0.4 + - - -
153B PHE* 4.2 4.0 - - - +
154B LYS* 3.4 45.8 - - + +
155B LYS 4.5 5.4 + - - +
157B ASP* 2.7 38.5 + - - +
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Residues in contact with ASP 163 (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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161A ILE* 3.8 2.1 - - - +
162A ARG* 1.3 81.1 - - - +
164A LYS* 1.3 69.9 + - - +
165A PRO* 3.4 23.0 - - + +
170A TRP* 3.5 8.0 - - - +
171A ASN* 2.9 36.5 + - + +
142B ASP* 4.8 5.7 - - - +
154B LYS* 3.9 32.8 + - + +
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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