Contacts of the strand formed by residues 164 - 169 (chain A) in PDB entry 2IHU
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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102A VAL 2.9 6.3 + - - -
103A ILE* 3.5 10.4 - - - +
104A ALA* 2.9 26.3 + - - +
134A LYS* 4.0 0.5 - - - +
135A TYR* 3.4 22.2 - - - +
152A ALA* 2.7 47.9 + - - -
155A ALA* 3.8 1.2 - - - +
156A ALA* 3.5 11.8 + - - +
162A GLY 3.9 0.4 + - - -
163A PRO* 1.3 74.5 + - - +
165A PHE* 1.3 60.6 + - - +
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Residues in contact with PHE 165 (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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85A MET* 3.9 10.5 - - + -
88A LEU* 5.3 1.1 - - + -
92A ILE* 4.3 10.1 - - + -
104A ALA* 3.2 24.2 - - + -
105A LEU 4.4 0.9 - - - -
106A ALA* 3.6 36.3 - - + -
125A SER* 3.8 40.6 - - - -
126A VAL* 4.1 3.1 - - + -
129A VAL* 3.5 31.2 - - + -
133A SER* 4.8 1.3 - - - +
135A TYR* 2.8 15.8 + - - +
136A ALA* 3.2 11.9 + - + -
137A VAL* 3.0 27.0 + - - +
164A SER* 1.3 74.3 - - - +
166A ILE* 1.3 66.0 + - - +
167A SER* 3.8 21.1 - - - -
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Residues in contact with ILE 166 (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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103A ILE* 4.7 2.7 - - + -
104A ALA 3.0 7.7 + - - -
105A LEU* 3.5 26.1 - - + -
106A ALA 3.1 24.1 + - - +
137A VAL* 3.4 22.4 - - + +
139A LEU 4.7 0.9 - - - +
145A ILE* 4.0 10.3 - - + -
148A LEU* 3.7 38.4 - - + +
149A VAL* 3.9 15.9 - - + +
152A ALA* 4.1 14.6 - - + -
165A PHE* 1.3 81.1 - - - +
167A SER* 1.3 65.8 + - - +
168A LEU* 3.8 25.4 - - + +
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Residues in contact with SER 167 (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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106A ALA 3.4 6.3 + - - -
107A ALA 4.5 0.5 + - - -
108A GLN* 3.4 24.1 + - - +
125A SER* 4.0 11.6 + - - -
126A VAL* 4.2 8.3 - - - -
137A VAL 2.8 14.9 + - - -
138A GLU* 3.5 11.5 + - - +
139A LEU* 3.0 28.8 + - - +
165A PHE* 3.8 20.7 - - - -
166A ILE* 1.3 73.5 - - - +
168A LEU* 1.3 61.9 + - - +
169A PRO* 3.5 2.6 - - - +
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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
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18A LEU* 3.8 13.0 - - + -
78A TRP* 3.5 36.8 - - + -
105A LEU* 4.0 17.0 - - + -
106A ALA 2.8 14.2 + - - +
107A ALA* 3.4 7.4 - - - +
108A GLN 2.8 18.5 + - - -
139A LEU* 4.0 14.6 - - + -
145A ILE* 3.6 31.6 - - + -
166A ILE* 3.8 15.9 - - + +
167A SER* 1.3 76.3 + - - +
169A PRO* 1.4 69.3 - - - +
170A VAL* 3.2 2.6 + - - -
173A LEU* 4.4 19.1 - - + +
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Residues in contact with PRO 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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108A GLN* 3.3 13.2 - - + +
109A SER 3.3 13.0 - - - +
111A SER* 3.8 6.5 - - - +
114A ILE* 4.1 15.3 - - + -
138A GLU* 4.0 13.2 - - + -
139A LEU* 3.5 27.6 - - + +
167A SER 3.5 11.4 - - - +
168A LEU* 1.4 82.2 - - - +
170A VAL* 1.3 65.5 + - - +
171A ASP* 3.2 14.1 - - - +
172A LEU* 3.0 16.1 + - + +
173A LEU* 3.0 19.6 + - - +
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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