Contacts of the strand formed by residues 179 - 183 (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 ARG 179 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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148B GLU 5.6 1.6 - - - +
149B GLU 5.5 0.5 - - - -
150B ASP 5.2 0.7 - - - +
151B LEU* 4.3 6.6 - - - +
160B ARG* 5.8 0.8 - - - +
162B ARG* 3.3 57.1 - - - +
171B ASN* 4.3 5.8 - - - +
172B ALA 3.3 6.3 - - - +
173B GLU* 3.9 11.9 + - - +
177B GLY 3.6 9.0 + - - +
178B LYS* 1.3 88.9 - - - +
180B GLY* 1.3 58.3 + - - +
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Residues in contact with GLY 180 (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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149B GLU 3.5 12.1 - - - -
150B ASP 4.2 0.9 - - - -
151B LEU* 3.7 16.5 - - - +
171B ASN* 3.7 13.8 - - - +
172B ALA* 3.0 29.8 + - - +
179B ARG* 1.3 76.6 - - - +
181B MET* 1.3 65.5 + - - -
182B ILE 3.8 0.2 + - - -
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Residues in contact with MET 181 (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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143B PHE* 3.9 2.6 - - - -
149B GLU* 3.0 31.9 + - + +
150B ASP* 3.3 20.6 - - - +
151B LEU 2.9 19.9 + - - +
165B PRO* 3.8 18.6 - - + -
166B GLU* 5.2 2.9 - - - +
169B TRP* 3.6 35.4 - - + +
170B TRP 3.3 19.5 - - - -
171B ASN* 3.6 27.8 - - - +
180B GLY* 1.3 73.0 - - - -
182B ILE* 1.3 59.5 + - - +
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Residues in contact with ILE 182 (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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137B VAL* 4.2 1.3 - - + -
151B LEU* 3.8 23.8 - - + +
153B PHE* 3.5 23.3 - - + -
159B LEU* 4.1 12.1 - - + -
161B ILE* 3.8 18.4 - - + -
169B TRP* 3.3 11.3 - - - -
170B TRP* 2.8 46.4 + - + +
172B ALA* 3.7 20.9 - - + -
181B MET* 1.3 78.3 - - - +
183B PRO* 1.4 69.8 - - + +
184B VAL* 3.5 1.4 + - - +
187B VAL* 4.1 26.7 - - + -
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Residues in contact with PRO 183 (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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143B PHE* 3.6 24.9 - - + -
153B PHE* 3.9 4.0 - - + -
168B GLN 3.4 7.2 - - - +
169B TRP* 3.7 8.2 - - + -
182B ILE* 1.4 87.1 - - + +
184B VAL* 1.3 65.1 + - - +
185B PRO* 3.3 1.8 - - + -
186B TYR* 3.0 34.4 + - + +
187B VAL* 4.0 7.1 + - - +
5N LEU* 3.5 33.2 - - + -
6N PRO* 3.7 17.3 - - + -
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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