Contacts of the strand formed by residues 164 - 168 (chain B) in PDB entry 4QKB
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 LEU 164 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34B VAL 3.8 0.9 - - - +
35B VAL* 3.5 1.0 - - - -
36B ARG* 2.6 46.8 + - + +
39B PHE* 3.8 34.3 - - + +
92B VAL* 4.0 22.7 - - + +
95B ALA* 4.1 25.8 - - + -
96B ALA* 5.0 0.7 - - + -
133B ALA* 4.3 2.7 - - + -
134B GLY 3.5 15.3 - - - +
135B LEU* 3.9 20.6 - - + -
163B SER* 1.3 74.8 - - - +
165B TYR* 1.3 68.2 + - - +
166B ILE* 4.2 18.2 - - + +
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Residues in contact with TYR 165 (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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34B VAL 3.1 10.1 - - - +
35B VAL* 4.3 5.2 - - + +
132B ILE* 4.6 13.9 - - + +
133B ALA* 3.3 4.3 - - - -
134B GLY* 2.8 72.2 + - - -
135B LEU 5.5 0.2 - - - -
136B SER* 4.7 2.2 - - - -
143B MSE 3.4 25.2 - - + +
157B LEU* 4.7 5.8 - - + -
159B LEU* 3.7 37.2 - - + -
163B SER* 4.2 1.4 + - - -
164B LEU* 1.3 75.8 - - - +
166B ILE* 1.3 64.8 + - - +
167B LEU* 3.9 25.6 - - + -
177B HIS* 6.3 0.2 - + - -
197B ARG* 4.2 3.8 - - - -
199B SER* 5.9 0.2 - - - -
201B ILE* 4.3 4.9 - - - +
302B AKG 2.2 44.8 + - - +
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Residues in contact with ILE 166 (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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32B ALA 3.3 4.7 - - - +
33B ALA* 3.4 1.6 - - - -
34B VAL* 2.7 54.8 + - + +
36B ARG* 5.0 7.2 - - - -
95B ALA 3.9 9.0 - - - +
96B ALA* 3.8 31.2 - - + -
131B THR* 4.0 14.8 - - + -
132B ILE 3.5 9.6 - - - +
133B ALA* 4.6 0.4 - - + -
164B LEU* 4.2 18.2 - - + +
165B TYR* 1.3 79.3 - - - +
167B LEU* 1.3 69.2 + - - +
168B ARG* 3.9 33.2 - - + +
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Residues in contact with LEU 167 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32B ALA 3.5 2.0 - - - -
33B ALA* 4.2 7.2 - - + -
130B ALA 3.8 0.5 - - - +
131B THR* 3.6 1.7 - - - +
132B ILE* 2.9 44.5 + - + +
143B MSE 4.1 9.0 - - - -
145B LEU* 3.9 36.1 - - + -
157B LEU* 4.1 15.3 - - + -
165B TYR* 3.9 18.1 - - + -
166B ILE* 1.3 81.1 - - - +
168B ARG* 1.3 62.1 + - - +
171B ALA* 4.3 13.0 - - + +
172B ARG* 4.0 7.4 - - + +
177B HIS* 3.4 34.8 - - + +
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Residues in contact with ARG 168 (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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31B ASP* 3.0 25.7 + - - +
32B ALA* 2.9 33.1 + - + +
34B VAL* 4.5 8.9 - - - +
95B ALA 4.6 4.6 + - - -
96B ALA* 3.1 30.9 + - - +
101B GLN* 6.1 0.8 - - - +
130B ALA 3.2 13.7 - - - +
131B THR* 4.3 11.8 + - + +
166B ILE* 3.9 21.9 - - + +
167B LEU* 1.3 74.5 - - - +
169B GLY* 1.3 69.0 + - - +
170B SER 3.2 1.0 + - - -
171B ALA* 3.2 17.0 + - - +
172B ARG* 4.0 2.5 - - - -
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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