Contacts of the strand formed by residues 164 - 168 (chain D) in PDB entry 2I6A
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 VAL 164 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8D ILE 3.4 1.6 + - - -
9D LEU* 3.3 9.3 - - + +
10D PHE 2.9 23.9 + - - -
162D ALA* 3.6 4.6 - - - +
163D ARG* 1.3 86.9 - - + +
165D CYS* 1.3 71.2 + - - +
192D ILE* 3.5 17.0 - - + +
194D THR* 4.4 4.7 - - + -
307D LEU* 4.2 19.3 - - + +
310D LEU* 3.5 35.2 - - + +
311D VAL* 3.7 33.9 - - + -
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Residues in contact with CYS 165 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9D LEU* 4.8 0.2 - - - -
10D PHE* 3.1 29.8 - - + +
159D VAL* 4.7 8.5 - - - -
162D ALA* 4.2 10.8 - - - -
164D VAL* 1.3 79.5 - - - +
166D TYR* 1.3 54.6 + - - +
167D ILE* 5.4 0.4 - - + -
182D VAL* 4.0 20.4 - - + -
185D HIS* 5.8 4.3 - - - -
186D ALA* 5.3 5.8 - - - -
191D ARG* 5.6 4.7 - - - -
192D ILE 2.8 13.9 + - - +
193D PHE* 4.1 18.4 - - + -
194D THR* 2.5 38.4 + - - +
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Residues in contact with TYR 166 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9D LEU* 4.6 4.0 - - + +
10D PHE 2.8 10.7 + - - +
11D GLY* 3.2 23.7 - - - -
65D SER* 4.8 3.6 + - - -
66D THR* 3.3 29.5 - - + +
69D SER* 3.9 16.5 + - - -
70D ILE* 5.0 3.6 - - + -
165D CYS* 1.3 73.5 - - - +
167D ILE* 1.3 70.6 + - - +
168D ALA* 4.1 10.2 - - - +
194D THR* 3.0 29.6 - - - +
195D LEU 4.0 3.8 - - - -
196D ASN* 2.9 39.6 + - + +
221D PHE* 3.7 24.0 - + - -
300D ASP* 5.5 0.3 + - - -
303D VAL* 3.4 17.9 - - + +
307D LEU* 3.7 30.7 - - + -
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Residues in contact with ILE 167 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10D PHE* 4.8 2.2 - - + -
12D MET* 3.2 47.6 - - + +
66D THR* 4.1 0.2 - - - -
165D CYS* 5.4 0.2 - - + -
166D TYR* 1.3 85.8 - - - +
168D ALA* 1.3 75.8 + - - +
171D PHE* 3.7 20.6 - - + -
179D VAL* 4.0 19.5 - - + -
182D VAL* 4.2 11.4 - - + -
193D PHE* 4.0 27.4 - - + -
194D THR 3.1 7.1 + - - -
195D LEU* 3.2 35.5 - - + +
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Residues in contact with ALA 168 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65D SER* 4.2 12.8 - - - +
66D THR* 2.8 35.4 + - - +
166D TYR* 4.1 10.6 - - - +
167D ILE* 1.3 82.8 - - - +
169D GLY* 1.3 59.4 + - - +
170D PHE* 2.9 16.5 + - + +
171D PHE* 3.1 12.1 + - + +
172D LEU* 4.4 0.9 + - - +
195D LEU* 4.6 1.0 - - - +
196D ASN* 3.9 8.3 - - - -
198D SER* 3.4 13.5 - - - +
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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