Contacts of the strand formed by residues 166 - 172 (chain A) in PDB entry 3T2D
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 PHE 166 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147A PHE* 3.3 57.9 - + + -
156A LEU* 4.1 14.6 - - + -
162A MET* 4.1 16.8 - - + -
165A GLY* 1.3 81.7 - - - -
167A ILE* 1.3 63.6 + - - +
168A PHE* 4.1 2.8 - - + -
181A LEU 3.9 0.7 - - - +
182A LYS* 3.4 4.5 - - - +
183A THR* 3.0 40.3 + - - +
205A VAL* 3.9 13.7 - - + -
206A PHE 3.5 18.4 - - - +
207A ARG* 3.7 18.6 - - + -
208A ARG* 4.1 3.1 + - - +
214A ALA* 4.4 0.7 - - + -
244A GLY 3.7 20.9 - - - -
245A LEU* 4.0 13.0 - - + -
246A PRO* 4.2 4.0 - - + -
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Residues in contact with ILE 167 (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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166A PHE* 1.3 75.6 - - - +
168A PHE* 1.3 63.9 + - - +
169A GLU 4.0 0.3 + - - -
180A LEU* 4.1 30.5 - - + -
181A LEU 3.5 8.3 - - - +
182A LYS* 4.3 17.9 - - + -
205A VAL* 3.2 7.0 - - - +
206A PHE* 2.8 53.6 + - + +
207A ARG 4.2 6.7 - - - +
208A ARG* 4.1 31.0 - - + +
211A GLY* 5.2 4.9 - - - -
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Residues in contact with PHE 168 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143A LEU 3.9 13.9 - - - -
144A TYR* 4.1 4.3 - - - -
147A PHE* 3.6 19.5 - - + -
148A ALA* 4.0 12.8 - - + -
166A PHE* 4.1 10.5 - - + -
167A ILE* 1.3 75.7 - - - +
169A GLU* 1.3 58.2 + - - +
170A VAL* 3.7 5.8 + - + +
179A TYR 3.4 2.3 - - - +
180A LEU* 3.4 7.9 - - - -
181A LEU* 2.8 42.0 + - + +
183A THR* 3.4 33.0 - - + -
190A LEU* 3.6 33.2 - - + -
202A ILE* 3.7 33.4 - - + -
204A LYS 3.8 3.4 - - - +
205A VAL* 4.0 17.0 - - + -
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Residues in contact with GLU 169 (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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167A ILE* 4.0 1.0 + - - +
168A PHE* 1.3 69.6 - - - +
170A VAL* 1.3 56.7 + - - +
178A VAL* 3.7 21.1 - - + -
179A TYR 3.5 3.6 - - - -
180A LEU* 3.9 14.2 - - + +
202A ILE* 3.7 1.6 - - - -
203A ARG* 2.8 72.9 + - + +
204A LYS* 2.8 37.9 + - + +
206A PHE* 3.8 21.8 - - + -
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Residues in contact with VAL 170 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168A PHE* 4.2 7.9 - - + +
169A GLU* 1.3 77.2 - - - +
171A LEU* 1.3 59.8 + - - +
172A ASP 4.0 0.2 + - - -
177A LYS 3.8 0.3 - - - +
178A VAL* 3.3 7.3 - - - +
179A TYR* 2.8 45.0 + - + +
181A LEU* 4.0 10.3 - - + -
190A LEU* 3.6 31.2 - - + -
193A LEU* 4.7 7.9 - - + -
194A ILE* 3.9 13.5 - - + -
200A TYR* 3.8 35.9 - - + -
201A ILE 3.4 8.5 - - - +
202A ILE* 4.5 5.4 - - + -
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Residues in contact with LEU 171 (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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169A GLU 4.1 0.8 + - - -
170A VAL* 1.3 74.1 - - - +
172A ASP* 1.4 67.0 + - - +
173A VAL* 3.4 25.7 + - + +
176A HIS* 4.2 19.5 - - + -
177A LYS 3.7 15.0 - - - +
178A VAL* 3.9 17.3 - - + +
199A ARG 3.2 4.3 - - - +
200A TYR* 3.4 0.5 - - - -
201A ILE* 2.9 36.1 + - - +
203A ARG* 3.7 37.9 - - + +
219A VAL* 4.1 14.4 - - + +
220A GLU* 4.1 4.3 - - - -
221A ARG* 4.1 16.8 - - - +
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Residues in contact with ASP 172 (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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170A VAL 4.0 1.0 + - - -
171A LEU* 1.4 69.8 - - - +
173A VAL* 1.3 57.8 + - - +
174A VAL 2.9 15.8 + - - -
175A GLU* 3.0 21.1 + - - +
176A HIS* 2.9 31.2 + - - -
177A LYS* 2.8 22.6 + - + +
179A TYR* 4.1 11.8 + - + -
199A ARG* 2.9 45.8 + - - +
200A TYR* 3.7 24.5 + - + -
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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