Contacts of the strand formed by residues 175 - 178 (chain O) in PDB entry 2GTL
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 ARG 175 (chain O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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168O GLU 4.1 0.3 - - - +
169O TYR* 3.7 4.1 - - - -
170O SER* 3.3 23.9 + - - -
173O ASP* 3.1 33.6 + - - +
174O HIS* 1.3 77.2 - - - +
176O LEU* 1.3 65.2 + - - +
177O THR* 3.8 13.7 + - - +
189O VAL* 3.9 26.5 - - + +
190O GLY 3.5 11.2 - - - +
191O GLU* 3.4 29.2 + - + +
210O GLU* 5.7 3.8 + - - -
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Residues in contact with LEU 176 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102O THR* 4.2 8.5 - - + +
127O LEU* 4.8 2.7 - - + -
129O PHE* 3.5 38.4 - - + -
144O LEU* 4.3 3.8 - - + -
168O GLU 3.2 12.6 - - - +
169O TYR* 3.8 20.5 - - + -
174O HIS 4.2 0.2 - - - -
175O ARG* 1.3 73.6 - - - +
177O THR* 1.3 59.7 + - - +
178O ILE* 3.9 23.5 + - + -
188O LEU* 4.2 2.4 - - + +
189O VAL* 3.7 2.9 - - - -
190O GLY* 3.0 52.7 + - - +
192O PHE* 5.1 7.4 - - + -
200O PHE* 4.3 15.7 - - + -
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Residues in contact with THR 177 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122J GLY* 5.9 3.6 - - - -
123J ARG* 5.3 9.4 - - + -
144O LEU* 5.9 0.2 - - - +
167O GLY* 3.1 4.3 - - - -
168O GLU* 2.9 42.1 + - - +
175O ARG* 4.1 17.3 + - - +
176O LEU* 1.3 75.0 - - - +
178O ILE* 1.3 65.0 + - - +
179O HIS* 3.8 8.3 + - + +
188O LEU 3.8 2.5 - - - +
189O VAL* 3.9 21.4 - - + +
207O GLU* 4.4 18.4 - - - +
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Residues in contact with ILE 178 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127O LEU* 3.9 33.9 - - + -
144O LEU* 5.8 1.8 - - + -
146O VAL* 3.6 38.1 - - + -
148O ILE* 4.1 13.5 - - + -
165O ALA* 3.9 9.0 - - + -
166O ASP 3.7 4.3 - - - +
167O GLY* 5.0 2.7 - - - -
176O LEU* 3.9 22.4 - - + -
177O THR* 1.3 75.0 - - - +
179O HIS* 1.3 74.5 + - - +
180O PRO 3.6 0.3 - - - -
181O PRO* 5.5 0.7 - - + -
187O GLY* 3.7 1.9 - - - -
188O LEU* 2.8 47.1 + - + +
207O GLU* 4.5 3.0 - - - +
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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