Contacts of the strand formed by residues 167 - 171 (chain B) in PDB entry 6D6U
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 167 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B ARG* 5.3 2.2 - - - +
39B THR* 3.6 15.3 - - + -
41B VAL* 4.2 14.6 - - + -
95B TRP* 4.8 7.2 - - + -
97B PRO* 5.5 3.8 - - + -
159B SER* 4.4 9.1 - - - +
162B TYR* 3.6 43.3 - - + +
163B THR 3.4 12.5 + - - +
164B ARG* 4.0 1.4 - - - +
166B GLU* 1.3 84.9 - - + +
168B VAL* 1.3 66.9 + - - +
169B TYR* 3.8 28.5 - - + +
211B VAL* 3.8 15.1 - - - +
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Residues in contact with VAL 168 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B VAL* 4.9 13.2 - - + -
39B THR 3.6 12.0 + - - +
40B GLU* 3.5 12.5 - - + +
41B VAL 3.1 21.5 + - - +
164B ARG* 3.3 34.1 - - + +
167B VAL* 1.3 75.3 - - - +
169B TYR* 1.3 74.5 + - - +
170B GLU* 4.0 14.6 - - + +
211B VAL* 4.5 9.0 - - + -
101J LEU* 6.1 6.1 - - + -
102J ARG* 5.9 3.4 - - - +
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Residues in contact with TYR 169 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41B VAL* 3.5 41.1 - - + +
43B THR* 4.3 9.2 - - - +
68B GLN* 5.5 0.4 - - - -
97B PRO* 4.7 4.3 - - + +
98B ASP 3.2 11.8 + - - -
99B THR* 2.6 32.5 + - + -
157B PHE* 4.5 4.3 - + - -
158B GLY* 3.6 11.4 - - - -
159B SER* 3.4 34.8 + - - -
167B VAL* 3.8 13.6 - - + +
168B VAL* 1.3 78.0 - - - +
170B GLU* 1.3 78.4 - - - +
211B VAL* 4.1 15.6 - - + +
213B MET* 3.8 44.7 - - + +
102J ARG* 5.6 0.5 + - - -
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Residues in contact with GLU 170 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40B GLU* 3.5 30.1 - - + +
41B VAL 3.1 7.7 + - - +
42B LYS* 3.3 10.5 - - + -
43B THR* 3.0 25.5 + - - -
168B VAL* 4.0 13.7 + - + +
169B TYR* 1.3 83.1 - - - +
171B TRP* 1.3 70.7 + - - +
200B SER* 5.6 2.1 + - - -
213B MET* 5.0 4.0 - - - -
32I TYR* 5.2 5.0 + - - -
99J LYS* 5.9 3.8 - - - +
101J LEU* 5.3 1.5 - - - +
102J ARG* 3.4 53.5 + - - +
103J TRP* 4.3 10.7 + - - +
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Residues in contact with TRP 171 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42B LYS* 5.2 1.9 - - - +
43B THR* 3.7 16.6 - - + -
44B ASP* 4.8 3.6 - - - -
45B ILE* 4.5 9.2 - - + -
157B PHE* 3.6 28.3 - + - -
170B GLU* 1.3 82.0 + - - +
172B THR* 1.3 67.9 + - - +
173B ARG 3.4 10.1 - - - +
175B PRO* 4.3 17.9 - - + -
178B SER* 3.3 30.1 - - - +
179B VAL* 4.0 19.3 - - + -
198B VAL* 4.3 18.2 - - + +
199B ASP 5.0 1.6 - - - +
200B SER* 3.5 11.4 + - - -
213B MET* 3.9 22.8 - - + -
214B THR 4.3 5.2 - - - -
215B THR* 3.7 22.7 - - - -
32I TYR* 3.3 27.8 + + - -
99J LYS* 5.4 1.7 + - - -
103J TRP* 3.6 14.6 + - - +
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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