Contacts of the strand formed by residues 31 - 36 (chain B) in PDB entry 4QYJ
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 THR 31 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29B GLY 4.4 5.4 - - - +
30B LYS* 1.3 79.2 - - - +
32B LEU* 1.3 63.0 + - - +
33B ASN* 5.7 0.4 - - - +
45B GLU* 3.6 35.8 + - + +
46B VAL* 3.0 22.1 + - - -
47B PRO* 4.6 0.5 - - - +
48B ASP* 3.6 13.8 - - - +
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Residues in contact with LEU 32 (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 THR* 1.3 77.7 - - - +
33B ASN* 1.3 74.8 + - - +
34B VAL* 3.8 6.5 + - + -
45B GLU* 3.3 4.3 - - - -
46B VAL* 3.0 41.7 + - + +
47B PRO 4.2 2.5 - - - +
48B ASP* 3.2 31.4 - - + +
195B GLU* 4.4 30.1 - - + +
198B PRO* 5.7 1.8 - - + -
222B THR* 6.3 0.7 - - - -
223B GLY* 3.7 11.7 - - - +
224B ARG* 3.5 22.2 - - + +
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Residues in contact with ASN 33 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B THR* 5.7 0.3 - - - +
32B LEU* 1.3 81.5 - - - +
34B VAL* 1.3 61.9 + - - +
35B TYR* 3.2 36.7 + - + +
42B ILE* 3.8 29.1 - - + +
44B THR 3.6 6.7 - - - +
45B GLU* 3.3 26.2 - - - +
195B GLU* 4.7 5.0 - - - +
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Residues in contact with VAL 34 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32B LEU* 4.7 3.6 - - + -
33B ASN* 1.3 74.7 - - - +
35B TYR* 1.3 69.5 + - - +
42B ILE* 3.6 2.9 - - - -
43B LEU* 2.9 29.3 + - + -
44B THR* 3.1 18.4 + - + +
46B VAL* 3.8 18.4 - - + -
103B ASN* 2.9 36.6 - - - +
195B GLU 4.0 9.4 - - - +
196B GLU* 4.1 5.4 - - - +
198B PRO* 3.3 34.8 - - + -
199B LEU* 4.7 4.5 - - + -
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Residues in contact with TYR 35 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B ASN* 3.2 40.3 + - + +
34B VAL* 1.3 79.0 - - - +
36B ASN* 1.3 69.0 + - - +
37B PRO* 4.0 1.2 - - + +
40B GLY 5.1 2.0 - - - -
41B ASP* 3.2 27.1 - - - +
42B ILE* 3.9 15.7 - - + -
43B LEU* 3.8 7.2 - - - +
103B ASN* 3.5 27.7 + - - +
196B GLU* 5.0 3.7 + - - +
344B VAL 6.1 0.7 - - - +
379B PHE* 5.4 11.9 - + + -
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Residues in contact with ASN 36 (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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35B TYR* 1.3 80.8 - - - +
37B PRO* 1.3 74.4 - - - +
38B ALA* 3.0 21.5 + - - +
39B THR* 3.3 40.6 + - - +
40B GLY* 3.8 3.1 - - - -
41B ASP* 2.9 12.1 + - + +
42B ILE 5.6 0.2 - - - +
43B LEU* 4.1 13.9 - - + +
101B THR 4.7 1.7 - - - +
102B LEU* 3.1 36.9 - - - +
379B PHE* 4.5 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