Contacts of the helix formed by residues 172 - 177 (chain X) in PDB entry 3EXG
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 ASN 172 (chain X).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5X VAL* 5.8 0.2 - - - +
117X PRO* 4.3 1.1 - - - -
118X ASN 4.1 12.7 - - - +
119X GLY* 5.6 0.2 - - - -
120X ALA 4.4 11.6 + - - +
147X PRO* 5.5 3.0 + - - +
171X GLU* 1.3 78.5 - - - +
173X GLU* 1.3 65.2 + - - +
174X LEU* 3.0 27.9 - - - +
175X MET* 3.1 31.9 + - + +
176X TYR* 3.4 15.4 + - - -
213X SER* 3.5 17.1 + - - +
214X ARG* 3.4 27.2 + - - +
215X PRO* 5.3 0.2 - - - +
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Residues in contact with GLU 173 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6X ARG* 5.2 1.1 + - - +
37X TYR* 3.5 42.9 + - + -
117X PRO* 3.7 16.5 - - + +
118X ASN 4.9 1.6 + - - -
121X SER* 2.8 31.8 + - - +
124X VAL* 5.6 0.7 - - - +
172X ASN* 1.3 74.4 - - - +
174X LEU* 1.3 71.6 + - + +
176X TYR* 3.0 33.5 + - + +
177X GLY 4.3 0.7 + - - -
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Residues in contact with LEU 174 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120X ALA 4.0 9.9 - - - +
121X SER* 3.7 29.4 - - - +
122X ALA* 4.0 22.7 - - + -
172X ASN* 3.0 9.8 - - - +
173X GLU* 1.3 84.7 - - - +
175X MET* 1.3 61.0 + - - +
176X TYR 3.3 0.7 + - - -
177X GLY* 4.0 4.9 + - - -
178X VAL* 3.9 11.9 - - - +
214X ARG* 3.4 42.4 - - - +
313X ILE* 5.9 0.9 - - + -
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Residues in contact with MET 175 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5X VAL* 3.0 22.1 - - + +
147X PRO 5.7 0.7 - - - +
148X TRP* 3.4 45.1 - - + +
172X ASN* 3.1 32.5 + - + +
174X LEU* 1.3 75.5 - - - +
176X TYR* 1.3 63.3 + - - +
177X GLY 3.2 0.2 - - - -
178X VAL* 3.0 26.7 + - + +
180X PHE* 3.7 31.9 - - + -
214X ARG* 4.0 27.6 - - + +
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Residues in contact with TYR 176 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4X THR* 3.4 1.7 - - - -
5X VAL* 3.3 11.2 + - + -
6X ARG* 2.9 54.6 + - + +
9X ILE* 3.7 25.6 - - + -
37X TYR* 3.8 35.5 - + + -
39X VAL* 3.6 24.6 - - + +
115X ARG* 4.0 1.6 + - - -
117X PRO* 3.6 18.2 - - + +
171X GLU* 2.5 37.1 + - + +
172X ASN 3.4 5.8 + - - -
173X GLU* 3.0 35.1 + - + +
175X MET* 1.3 75.9 - - - +
177X GLY* 1.3 62.0 + - - +
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Residues in contact with GLY 177 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4X THR* 3.1 14.4 - - - +
6X ARG* 3.6 19.2 - - - +
173X GLU 4.3 0.8 + - - -
174X LEU 4.0 5.1 + - - -
175X MET 3.2 0.4 - - - -
176X TYR* 1.3 79.3 - - - +
178X VAL* 1.3 63.3 + - - +
179X PRO* 3.4 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