Contacts of the strand formed by residues 172 - 176 (chain C) in PDB entry 4G7H
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 172 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160C ALA 3.7 0.7 - - - +
161C SER* 3.6 0.2 - - - -
162C ILE* 2.8 46.7 + - + +
170C PRO* 3.7 14.3 + - + +
171C TRP* 1.3 75.0 - - - +
173C ASP* 1.3 69.1 + - - +
174C LEU* 3.5 28.3 - - + -
184C MET* 3.9 16.4 - - + -
185C LYS 3.4 2.0 - - - -
186C VAL* 3.3 24.7 - - + -
261C ILE* 4.1 18.2 - - + -
267C TYR* 4.9 1.8 - - + +
290C LEU* 3.4 32.5 - - + -
303C PHE* 4.4 8.7 - - + -
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Residues in contact with ASP 173 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159C ILE* 3.8 24.1 - - + +
160C ALA 3.2 2.7 - - - +
161C SER* 3.5 19.2 + - - -
171C TRP* 4.0 7.8 + - - +
172C ILE* 1.3 84.0 - - - +
174C LEU* 1.3 62.4 + - - +
175C GLU* 4.0 3.7 + - + +
183C SER 3.6 1.7 - - - +
184C MET* 3.4 4.5 - - - -
185C LYS* 2.9 64.3 + - + +
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Residues in contact with LEU 174 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159C ILE* 3.8 4.6 - - - +
160C ALA* 2.8 47.2 + - + +
162C ILE* 5.0 5.4 - - + -
172C ILE* 3.5 26.2 - - + -
173C ASP* 1.3 72.6 - - - +
175C GLU* 1.3 61.3 + - - +
182C VAL* 5.3 1.1 - - + -
183C SER 3.5 3.1 - - - +
184C MET* 4.2 19.3 - - + -
193C LEU* 3.9 28.0 - - + -
303C PHE* 4.5 9.4 - - + +
306C THR* 3.3 30.1 - - - +
307C LEU* 4.3 12.8 - - + +
310C LEU* 3.8 12.2 - - + +
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Residues in contact with GLU 175 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151C ASP* 4.0 12.9 - - - +
154C ARG* 5.2 4.5 - - - -
158C TYR 4.5 4.9 - - - +
159C ILE* 3.6 30.4 - - + +
173C ASP* 5.1 4.0 - - + +
174C LEU* 1.3 74.8 - - - +
176C VAL* 1.3 73.1 + - - +
177C GLU* 3.4 24.5 - - - +
178C PRO* 5.7 0.2 - - - +
182C VAL* 3.3 7.2 - - - +
183C SER* 2.9 42.6 + - - +
185C LYS* 4.1 15.1 + - - -
190C LYS* 3.6 14.2 + - - -
310C LEU* 4.6 1.3 - - - +
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Residues in contact with VAL 176 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154C ARG* 3.2 19.8 + - - -
157C ARG* 3.3 34.2 - - + +
158C TYR 4.6 5.6 + - - +
175C GLU* 1.3 83.0 - - - +
177C GLU* 1.3 67.9 + - - +
180C GLY* 4.2 17.9 - - - +
181C VAL 4.1 2.9 - - - +
182C VAL* 4.5 5.2 - - + +
217C LEU* 4.8 12.3 - - + -
310C LEU* 4.4 15.3 - - + -
311C PHE* 3.7 32.1 - - + -
314C THR* 5.3 5.4 - - + +
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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