Contacts of the strand formed by residues 170 - 174 (chain C) in PDB entry 1GZ0
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 TRP 170 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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168C ASN 3.9 1.4 + - - -
169C ILE* 1.3 73.8 - - - +
171C ILE* 1.3 59.8 + - - +
172C VAL* 3.5 23.0 - - + +
186C LYS 4.8 7.9 + - - -
188C THR 5.6 2.5 - - - +
190C ARG 2.7 19.5 + - - +
191C LEU* 3.2 10.2 - - + +
192C ALA 2.8 27.0 + - - -
211C ASP* 3.7 28.7 - - + -
212C GLU* 2.8 42.7 + - + +
130D ARG* 3.7 32.8 - - - -
200D GLU* 3.5 44.3 + - + -
201D GLY 4.5 0.9 - - - -
202D MSE 4.6 2.7 - - - -
203D ARG* 3.7 26.5 - - + +
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Residues in contact with ILE 171 (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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99C ILE* 4.9 1.1 - - + -
161C MSE 3.5 42.6 - - + +
164C LEU* 4.2 13.2 - - + -
165C GLN* 3.4 33.0 - - + +
169C ILE* 3.8 9.0 - - + +
170C TRP* 1.3 79.7 - - - +
172C VAL* 1.3 61.7 + - - +
192C ALA* 3.3 14.4 - - + +
194C VAL* 3.7 25.8 - - + -
210C CYS* 3.7 7.1 - - - +
211C ASP* 2.9 38.5 + - - +
212C GLU* 3.2 9.0 + - - +
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Residues in contact with VAL 172 (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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170C TRP* 3.5 13.5 - - + +
171C ILE* 1.3 72.8 - - - +
173C GLY* 1.3 56.1 + - - +
185C SER* 4.1 5.6 - - - +
186C LYS 5.3 0.4 - - - +
187C MSE 4.6 7.0 - - + -
191C LEU* 3.2 36.8 - - + -
192C ALA 2.8 8.4 + - - +
193C LEU* 3.4 8.9 - - + +
194C VAL* 2.6 35.4 + - - +
212C GLU* 3.5 19.7 - - - +
214C ILE* 3.5 43.1 - - + -
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Residues in contact with GLY 173 (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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172C VAL* 1.3 75.2 - - - +
174C THR* 1.3 63.2 + - - -
194C VAL* 3.5 11.2 - - - -
202C MSE 3.7 11.2 - - - -
210C CYS* 3.8 12.5 - - - -
212C GLU 2.9 10.7 + - - -
213C LEU* 3.3 7.3 - - - -
214C ILE* 2.8 29.9 + - - +
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Residues in contact with THR 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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173C GLY* 1.3 72.3 - - - -
175C ALA* 1.3 70.9 + - - +
193C LEU* 4.5 1.0 - - - +
194C VAL 3.0 14.8 + - - -
195C MSE 3.8 26.8 - - + -
196C GLY 4.9 2.8 + - - +
202C MSE 3.0 23.0 - - - +
214C ILE* 3.3 19.4 - - - +
215C SER* 5.0 1.3 - - - -
216C ILE* 4.2 24.0 - - + +
234C CYS* 3.9 13.7 - - - -
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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