Contacts of the strand formed by residues 87 - 92 (chain B) in PDB entry 3QEK
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 87 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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28B ASN* 3.3 14.1 - - + -
29B ILE 4.0 3.6 - - - -
30B GLY* 3.6 24.9 - - - +
63B THR* 4.2 11.0 - - - +
82B LEU* 3.4 30.5 - - + +
83B ILE* 4.3 8.2 + - + +
85B SER 4.6 0.7 - - - +
86B GLN* 1.3 78.2 - - - +
88B TYR* 1.3 61.4 + - - +
89B ALA 3.8 10.3 - - - +
90B ILE* 3.9 27.4 - - + -
116B ILE* 4.2 14.0 - - + +
325B PRO* 3.3 15.2 - - - +
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Residues in contact with TYR 88 (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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25B LYS* 3.4 16.1 + - - -
26B ILE 4.8 2.7 + - - -
27B VAL* 3.6 32.0 - - + +
28B ASN 2.8 14.4 + - - +
29B ILE* 4.5 2.9 - - + -
86B GLN* 3.6 15.0 - - + -
87B VAL* 1.3 71.9 - - - +
89B ALA* 1.3 61.9 + - - +
116B ILE* 4.0 2.5 - - - -
117B PRO* 3.4 5.5 - - - +
313B ILE* 3.6 27.8 - - + -
316B LEU* 4.6 3.8 - - + -
317B PHE* 3.8 20.9 - + - -
322B ILE* 5.0 0.2 - - + -
323B THR 4.6 3.1 + - - -
324B ASP* 3.2 24.3 + - - -
325B PRO* 3.4 18.7 - - + +
336B TRP* 3.3 50.1 - + + -
342B PHE* 3.3 9.6 - - + -
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Residues in contact with ALA 89 (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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28B ASN 4.4 1.0 + - - -
29B ILE* 3.8 6.0 - - + +
30B GLY* 2.7 32.6 + - - -
87B VAL* 3.4 2.6 - - - +
88B TYR* 1.3 80.7 - - - +
90B ILE* 1.3 62.2 + - - +
91B LEU* 5.2 0.2 - - + -
116B ILE* 3.8 2.9 - - - +
117B PRO* 3.3 17.7 - - + +
119B ILE* 4.6 16.8 - - + -
309B VAL* 4.7 14.4 - - + -
342B PHE* 4.1 13.9 - - + -
346B LEU* 4.8 0.2 - - + -
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Residues in contact with ILE 90 (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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30B GLY* 3.3 6.1 - - - +
32B VAL* 4.1 2.7 - - + -
78B VAL* 3.9 20.4 - - + -
82B LEU* 3.8 35.0 - - + -
83B ILE* 5.1 2.5 - - + -
87B VAL* 3.9 21.1 - - + -
89B ALA* 1.3 80.3 - - - +
91B LEU* 1.3 71.7 + - - +
92B VAL* 3.9 11.7 - - + -
107B ILE* 4.0 6.5 - - + -
111B ALA* 4.0 18.6 - - + -
116B ILE* 4.2 5.8 - - + -
117B PRO 2.9 10.7 + - - +
118B VAL* 3.3 10.6 - - + +
119B ILE* 2.8 30.2 + - - -
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Residues in contact with LEU 91 (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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29B ILE* 4.1 16.8 - - + -
30B GLY 2.9 17.0 + - - +
31B ALA* 3.2 7.8 - - + -
32B VAL 2.7 32.7 + - - -
33B LEU* 4.9 0.4 - - + -
42B PHE* 3.8 26.2 - - + -
89B ALA 5.2 0.4 - - - -
90B ILE* 1.3 76.7 - - - +
92B VAL* 1.3 59.1 + - - +
119B ILE* 3.3 26.7 - - + +
121B LEU* 4.1 18.4 - - + -
302B ILE* 4.2 6.3 - - + +
305B ALA* 3.7 27.1 - - + -
306B VAL* 3.9 10.5 - - + -
309B VAL* 4.2 9.0 - - + -
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Residues in contact with VAL 92 (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 VAL* 3.4 5.4 - - + +
67B HIS* 4.1 5.2 - - - +
90B ILE* 3.9 4.0 - - + -
91B LEU* 1.3 82.2 - - - +
93B SER* 1.3 75.4 + - - +
104B PRO* 4.2 20.9 - - + +
107B ILE* 3.5 52.7 - - + -
118B VAL* 3.7 18.6 - - + -
119B ILE 2.9 10.7 + - - +
120B GLY* 3.5 5.8 - - - -
121B LEU* 2.8 28.9 + - - +
122B THR 4.2 0.5 + - - -
123B THR* 5.4 0.7 + - - +
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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