Contacts of the strand formed by residues 180 - 184 (chain B) in PDB entry 4IOP
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 VAL 180 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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122B LEU* 5.5 1.8 - - + -
126B GLN* 5.2 3.1 - - - +
137B ILE* 4.0 16.6 - - + -
161B PHE* 3.6 47.3 - - + -
162B SER 4.2 3.0 + - - +
163B VAL* 3.1 11.0 - - + -
164B ILE* 2.8 24.1 + - - +
173B ALA* 4.1 6.5 - - + -
174B VAL 3.4 15.9 - - - +
175B ILE* 4.1 20.9 - - + -
179B TRP* 1.3 82.7 - - - +
181B TYR* 1.3 67.5 + - - +
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Residues in contact with TYR 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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160A PHE* 3.8 18.8 - - + -
161A ILE* 3.2 37.2 - - + +
162A ASP* 3.0 49.9 + - - +
163B VAL* 4.5 2.3 - - - +
164B ILE* 3.4 33.7 - - + +
173B ALA* 3.7 5.4 - - - +
174B VAL* 3.2 31.5 + - + +
176B THR* 3.3 19.3 - - + -
179B TRP* 3.6 34.0 - + + +
180B VAL* 1.3 78.6 - - - +
182B SER* 1.3 62.0 + - - +
183B GLU* 5.2 0.2 - - - +
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Residues in contact with SER 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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158A ARG* 3.1 29.0 + - - +
160A PHE* 4.9 2.8 - - - +
148B TRP* 3.0 35.3 - - - -
163B VAL* 4.4 3.6 - - - -
164B ILE 3.2 14.1 + - - +
165B GLY* 4.3 4.0 - - - -
166B PRO* 3.3 23.3 + - - +
171B SER* 3.6 4.5 - - - -
172B CYS 3.6 3.1 - - - -
181B TYR* 1.3 76.8 - - - +
183B GLU* 1.3 66.0 + - - +
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Residues in contact with GLU 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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157A SER* 2.7 27.9 + - - -
158A ARG* 3.2 40.0 + - - +
159A GLY 4.4 0.3 + - - -
160A PHE* 4.7 1.2 + - - +
161A ILE* 3.8 16.7 + - + +
136B TRP* 4.7 2.5 - - + -
171B SER* 3.3 6.4 - - - -
172B CYS* 2.9 36.8 + - - +
174B VAL* 4.1 23.8 - - + -
181B TYR* 4.3 0.7 + - - +
182B SER* 1.3 79.7 - - - +
184B ASP* 1.3 65.3 + - - +
185B CYS 3.3 0.7 + - - -
187B SER* 5.5 0.7 + - - -
189B PHE* 3.6 31.9 - - + -
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Residues in contact with ASP 184 (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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143A ASN* 3.1 27.2 + - - +
144A GLY* 5.9 1.6 - - - -
158A ARG* 3.6 13.7 - - + +
136B TRP* 3.8 3.4 - - - -
170B ARG* 3.0 43.4 + - - +
183B GLU* 1.3 75.4 + - - +
185B CYS* 1.3 53.1 + - - +
186B SER* 2.7 34.2 + - - -
187B SER* 2.7 44.4 + - - +
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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