Contacts of the strand formed by residues 175 - 179 (chain A) in PDB entry 5IWG
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 175 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165A ILE* 4.1 28.0 - - + -
168A LEU* 4.0 31.6 - - + -
169A LEU* 3.8 21.8 - - + -
172A HIS* 4.0 17.7 - - + -
174A ARG* 1.3 78.5 - - - +
176A LEU* 1.3 70.9 + - - +
197A ARG 3.0 9.1 + - - +
198A VAL* 3.2 6.0 - - + +
199A MET 3.1 23.6 + - - -
257A TYR* 3.5 3.8 - - - -
261A ALA* 3.5 12.3 - - + +
263A VAL* 4.3 2.9 - - + -
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Residues in contact with LEU 176 (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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175A VAL* 1.3 75.7 - - - +
177A TYR* 1.3 56.8 + - - +
178A ILE* 3.9 21.3 - - + -
199A MET* 3.6 21.5 - - + +
201A VAL* 3.7 17.0 - - + -
250A ILE* 5.1 1.8 - - + -
253A VAL* 3.5 34.3 - - + -
254A MET* 3.7 36.1 - - + -
257A TYR* 4.4 3.1 - - + -
259A PRO* 3.7 18.5 - - + +
261A ALA 3.0 9.2 + - - +
262A VAL* 3.3 6.0 - - + +
263A VAL 2.8 31.9 + - - +
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Residues in contact with TYR 177 (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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145A HIS* 3.7 3.3 - - - +
161A ILE* 3.4 39.1 - - + +
165A ILE* 4.1 15.5 - - + -
175A VAL 4.0 0.6 + - - -
176A LEU* 1.3 71.5 - - - +
178A ILE* 1.3 59.6 + - - +
179A ASP* 2.5 42.9 + - + -
185A GLY* 4.9 4.7 - - - -
188A VAL* 3.5 30.3 - - + -
198A VAL* 4.5 1.8 - - + -
199A MET 2.8 15.5 + - - +
200A THR* 4.1 18.8 - - + -
201A VAL* 2.7 36.6 + - - +
202A SER* 5.9 1.1 - - - -
263A VAL* 3.4 20.0 - - + -
265A GLN* 3.3 24.1 - - + +
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Residues in contact with ILE 178 (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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176A LEU* 3.9 27.4 - - + -
177A TYR* 1.3 79.0 - - - +
179A ASP* 1.3 59.5 + - - +
180A ILE* 4.4 2.0 - - + -
201A VAL* 3.3 5.6 - - + +
203A PHE* 4.2 7.2 - - + -
246A PHE* 3.9 24.5 - - + -
250A ILE* 3.7 27.8 - - + -
262A VAL* 4.0 12.1 - - + -
263A VAL 2.9 7.9 + - - +
264A LEU* 3.4 22.4 - - + +
265A GLN* 2.8 32.6 + - - +
293A VAL* 3.6 26.5 - - + -
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Residues in contact with ASP 179 (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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145A HIS* 2.6 20.9 + - - -
177A TYR* 2.5 35.2 + - + +
178A ILE* 1.3 75.8 - - - +
180A ILE* 1.3 59.6 + - - +
181A ASP* 3.2 17.3 - - - +
185A GLY* 3.4 8.1 - - - -
201A VAL 2.9 12.6 + - - +
202A SER* 4.1 9.4 - - - +
203A PHE* 3.1 21.5 + - - -
265A GLN* 3.8 7.0 - - - -
402A CA 2.4 35.9 - - - -
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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