Contacts of the strand formed by residues 167 - 171 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31D ARG* 4.6 3.8 - - - -
39D THR* 3.3 13.0 - - - +
41D VAL* 4.3 9.9 - - + -
95D TRP* 4.4 17.7 - - + -
97D PRO* 5.6 2.5 - - + -
159D SER* 4.1 12.2 - - - +
162D TYR* 3.9 34.4 - - + +
163D THR 3.4 11.5 + - - +
164D ARG* 4.0 3.0 + - - +
166D GLU* 1.3 86.0 - - + +
168D VAL* 1.3 68.5 + - - +
169D TYR* 3.7 29.6 - - + -
211D VAL* 3.6 14.7 - - - +
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Residues in contact with VAL 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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38D VAL* 4.4 18.4 - - + -
39D THR 3.1 8.3 + - - +
40D GLU* 3.4 13.2 - - + +
41D VAL 3.2 22.9 + - - +
164D ARG* 3.6 28.7 - - + +
167D VAL* 1.3 78.8 - - - +
169D TYR* 1.3 74.0 + - - +
170D GLU* 3.9 15.7 - - + +
211D VAL* 4.3 11.2 - - + -
101K LEU* 5.8 8.1 - - + -
102K ARG* 6.0 0.9 - - - +
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Residues in contact with TYR 169 (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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41D VAL* 3.5 39.5 - - + +
43D THR* 4.3 7.6 - - - +
68D GLN* 5.2 0.2 - - - -
97D PRO* 4.7 3.9 - - + +
98D ASP 3.7 2.4 + - - -
99D THR* 2.5 38.5 + - + -
157D PHE* 4.4 8.5 - + - -
158D GLY* 3.7 11.9 - - - -
159D SER* 3.5 38.6 + - - -
167D VAL* 3.7 14.8 - - + -
168D VAL* 1.3 78.9 - - - +
170D GLU* 1.3 76.0 + - - +
211D VAL* 4.0 14.6 - - + +
213D MET* 3.5 45.3 - - + +
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Residues in contact with GLU 170 (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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40D GLU* 3.6 27.1 - - + +
41D VAL 3.1 7.6 + - - +
42D LYS* 3.2 12.4 - - + +
43D THR* 3.1 20.8 + - - -
168D VAL* 3.9 13.8 - - + +
169D TYR* 1.3 84.4 - - - +
171D TRP* 1.3 69.4 + - - +
200D SER* 4.9 5.6 + - - -
213D MET* 4.9 3.1 - - - -
99K LYS* 5.7 5.6 - - - +
101K LEU* 3.0 32.3 - - + +
102K ARG* 3.7 24.6 + - - -
103K TRP* 4.1 17.2 + - - +
32L TYR* 5.2 1.7 + - - -
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Residues in contact with TRP 171 (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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42D LYS* 5.0 2.0 - - - +
43D THR* 3.7 21.5 - - - +
44D ASP* 4.6 9.0 - - - -
45D ILE* 4.7 6.1 - - + -
157D PHE* 3.8 21.3 - + - -
170D GLU* 1.3 79.7 + - - +
172D THR* 1.3 65.7 + - - +
173D ARG 3.4 6.5 - - - +
175D PRO* 4.6 13.5 - - + -
178D SER* 3.6 30.1 - - - +
179D VAL* 3.7 22.7 - - + -
198D VAL* 4.0 15.3 - - + +
199D ASP 4.9 3.0 - - - +
200D SER* 4.3 1.5 + - - +
213D MET* 3.3 35.9 - - + -
214D THR 3.9 18.8 + - - -
215D THR* 3.6 16.6 - - - -
99K LYS* 4.7 1.6 + - - -
103K TRP* 3.3 23.1 + - - +
32L TYR* 3.6 24.4 + - - -
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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