Contacts of the strand formed by residues 171 - 177 (chain Y) in PDB entry 1T6B
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 ALA 171 (chain Y).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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131Y ILE* 4.1 17.7 - - + -
141Y SER* 3.2 28.0 - - - +
142Y ILE 4.6 1.1 - - - +
143Y ILE* 4.8 4.5 - - + -
166Y SER* 3.4 19.3 + - - +
167Y ARG* 3.5 25.8 + - - +
169Y LEU 3.4 2.0 - - - +
170Y GLY* 1.3 79.6 - - - +
172Y SER* 1.3 62.8 + - - +
173Y VAL* 4.9 0.6 - - - +
191Y ASP* 4.8 0.3 - - - +
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Residues in contact with SER 172 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141Y SER 3.2 10.7 + - - -
142Y ILE* 3.6 10.0 - - - +
143Y ILE 2.8 27.0 + - - +
170Y GLY 5.3 0.2 + - - -
171Y ALA* 1.3 75.0 - - - +
173Y VAL* 1.3 61.9 + - - +
174Y TYR* 3.9 22.0 + - - -
191Y ASP* 3.3 19.3 - - - -
195Y GLN* 5.3 1.6 - - - -
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Residues in contact with VAL 173 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124Y LEU* 4.6 7.4 - - + -
143Y ILE* 3.5 21.5 - - + +
145Y ALA* 5.5 1.1 - - + -
163Y ALA* 4.2 3.8 - - + +
166Y SER* 3.8 29.8 - - - +
167Y ARG* 3.8 18.4 - - + +
171Y ALA 4.9 0.4 - - - +
172Y SER* 1.3 77.4 - - - +
174Y TYR* 1.3 70.1 + - - +
175Y CYS* 4.6 0.4 - - - -
189Y ILE* 3.8 37.0 - - + +
190Y ALA* 3.3 5.2 - - - +
191Y ASP* 3.0 30.3 + - - +
195Y GLN* 3.4 8.0 - - - +
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Residues in contact with TYR 174 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142Y ILE* 4.1 20.4 - - + +
143Y ILE 2.8 18.9 + - - +
144Y ILE* 4.2 14.4 - - + -
145Y ALA* 2.9 27.7 + - - +
172Y SER* 4.0 23.2 - - - -
173Y VAL* 1.3 77.8 - - - +
175Y CYS* 1.3 67.0 + - - +
176Y VAL* 5.4 1.6 - - + -
195Y GLN* 3.3 50.9 + - + +
197Y PHE* 3.9 6.3 - + - -
206Y LEU* 3.5 20.0 - - + -
209Y ILE* 3.5 40.6 + - + +
210Y ILE* 4.9 4.4 - - + +
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Residues in contact with CYS 175 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145Y ALA* 3.4 13.5 - - + +
147Y THR* 5.4 1.1 - - + -
173Y VAL* 4.6 0.7 - - - -
174Y TYR* 1.3 80.5 - - - +
176Y VAL* 1.3 65.0 + - - +
177Y GLY 3.8 0.2 + - - -
186Y LEU* 3.8 38.1 - - + -
189Y ILE* 3.5 33.4 - - - -
190Y ALA* 3.7 17.2 - - + +
195Y GLN 2.8 10.0 + - - +
196Y VAL* 3.3 7.2 - - + +
197Y PHE* 3.0 25.3 + - - +
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Residues in contact with VAL 176 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65Y PHE* 4.0 22.2 - - + -
144Y ILE* 3.7 27.1 - - + -
145Y ALA 2.8 9.3 + - - +
146Y LEU* 3.6 12.0 - - + -
147Y THR* 3.4 22.7 + - - +
174Y TYR* 5.3 1.8 - - + -
175Y CYS* 1.3 77.0 - - - +
177Y GLY* 1.3 61.2 + - - +
178Y VAL* 4.1 1.0 - - - +
186Y LEU* 4.6 1.6 - - - +
197Y PHE* 3.1 14.1 - - + +
198Y PRO 3.7 5.2 - - - +
199Y VAL* 3.3 42.6 - - + +
202Y GLY 5.7 0.9 - - - +
206Y LEU* 4.8 5.4 - - + -
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Residues in contact with GLY 177 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147Y THR 3.5 5.4 - - - -
175Y CYS 3.8 1.2 + - - -
176Y VAL* 1.3 71.0 - - - +
178Y VAL* 1.3 60.3 + - - -
179Y LEU 4.3 0.3 + - - +
181Y PHE* 3.5 30.2 - - - -
186Y LEU* 4.0 7.5 - - - +
197Y PHE 2.6 16.8 + - - -
198Y PRO* 3.7 2.4 - - - +
199Y VAL* 2.8 31.1 + - - +
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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