Contacts of the strand formed by residues 175 - 179 (chain A) in PDB entry 4HXG
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 175 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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121A VAL* 5.1 3.6 - - - -
154A PHE* 3.5 14.0 - - - -
173A PHE 4.1 1.5 + - - -
174A SER* 1.3 75.0 - - - +
176A GLY* 1.3 68.3 + - - +
177A ILE* 5.0 2.4 - - - +
185A VAL* 3.4 5.4 - - - +
186A SER* 2.9 41.5 + - - +
220A TYR* 5.3 10.1 - - - -
221A ALA 4.9 7.9 + - - -
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Residues in contact with GLY 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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108A SER* 5.4 0.9 + - - -
110A GLU* 4.3 2.3 - - - +
119A LEU* 3.9 12.8 - - - +
121A VAL* 4.0 11.9 - - - +
154A PHE* 3.6 16.1 - - - -
175A SER* 1.3 81.9 + - - +
177A ILE* 1.3 70.5 + - - +
183A ILE* 4.6 1.8 - - - -
184A VAL 3.1 12.3 - - - -
185A VAL* 4.4 0.4 - - - -
186A SER* 4.9 0.4 - - - -
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Residues in contact with ILE 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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110A GLU* 3.5 15.7 - - - +
119A LEU* 3.9 7.5 - - - +
175A SER* 5.0 3.4 - - - +
176A GLY* 1.3 82.6 - - - +
178A TRP* 1.3 68.1 + - - +
183A ILE* 3.4 3.7 - - - +
184A VAL* 2.9 47.8 + - + +
221A ALA* 4.1 26.5 - - + +
222A ILE* 4.2 7.6 - - - +
223A ASP* 3.3 46.2 - - - +
224A SER* 3.9 3.8 - - - +
229A ILE* 5.1 0.4 - - + -
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Residues in contact with TRP 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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110A GLU* 3.2 44.1 + - - +
111A TRP 2.9 26.0 - - - +
112A ASN* 3.3 43.2 - - + +
117A ARG* 3.7 19.5 - - + -
118A LEU 4.1 4.9 - - - -
119A LEU* 3.2 25.3 - - + +
156A VAL* 4.0 29.2 - - + -
177A ILE* 1.3 78.1 - - - +
179A HIS* 1.3 58.2 + - - +
180A GLY 3.8 7.4 - - - +
181A ASP 3.9 13.7 - - - -
182A SER 3.2 22.9 - - - -
183A ILE* 3.7 17.9 - - + -
224A SER* 3.3 20.6 - - - -
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Residues in contact with HIS 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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177A ILE 3.4 1.6 + - - -
178A TRP* 1.3 75.0 - - - +
180A GLY* 1.3 60.2 + - - +
181A ASP 3.2 0.2 + - - -
182A SER* 2.8 38.9 + - - +
184A VAL* 3.4 21.5 - - + -
204A LEU* 4.5 15.5 - - + -
224A SER* 2.8 21.6 + - - -
226A GLY* 3.2 30.0 + - - -
227A GLU 3.8 16.8 + - - -
228A ARG 3.9 0.9 - - - -
229A ILE* 3.5 34.3 - - + +
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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