Contacts of the strand formed by residues 750 - 755 (chain B) in PDB entry 2EYQ
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 ASP 750 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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581B PHE* 4.3 14.4 + - - +
583B PHE* 3.7 26.4 - - + -
616B MET* 4.1 12.2 - - + +
620B LEU 4.0 4.7 - - - +
621B ALA* 3.9 8.2 - - - +
622B MET* 3.0 37.9 + - + +
724B GLY 3.8 10.3 - - - +
725B LEU* 4.1 11.0 - - + -
726B LEU* 3.0 28.2 + - - +
749B VAL* 1.3 83.0 - - - +
751B ILE* 1.3 60.7 + - - +
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Residues in contact with ILE 751 (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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622B MET* 3.0 38.3 + - - +
623B ASP* 3.4 20.6 - - - +
624B ARG 3.4 7.1 + - - -
725B LEU* 4.6 1.8 - - - -
726B LEU* 3.0 46.4 - - + -
728B VAL* 4.9 6.3 - - + -
742B ILE* 5.6 2.2 - - + +
745B MET 5.2 0.2 - - - +
746B ARG* 3.8 41.3 - - + +
749B VAL 4.1 4.0 - - - +
750B ASP* 1.3 76.1 - - - +
752B LEU* 1.3 65.8 + - - +
753B THR* 3.8 17.9 - - - +
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Residues in contact with LEU 752 (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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612B VAL* 4.0 28.7 - - + -
622B MET* 4.9 3.8 - - - -
624B ARG* 3.5 15.7 - - + +
626B VAL* 4.4 8.3 - - + -
637B VAL* 4.3 7.2 - - + -
638B ALA* 4.3 13.9 - - + -
641B ALA* 4.1 21.8 - - + -
725B LEU* 4.4 7.2 - - + -
726B LEU 2.9 10.5 + - - +
727B ILE* 3.3 22.7 - - + +
728B VAL* 2.9 25.6 + - - +
751B ILE* 1.3 78.0 - - - +
753B THR* 1.3 71.5 + - - +
754B LEU* 4.2 11.0 - - + -
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Residues in contact with THR 753 (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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624B ARG 2.8 12.0 + - - +
625B LEU* 3.2 28.1 - - + -
626B VAL 3.0 22.5 + - - -
728B VAL* 3.3 13.6 - - - +
731B GLU* 4.1 32.0 + - + +
746B ARG* 4.4 5.0 + - - -
751B ILE* 3.8 14.7 - - - +
752B LEU* 1.3 77.4 - - - +
754B LEU* 1.3 75.9 + - - +
755B THR* 5.7 0.4 - - - -
771B ARG* 4.5 5.4 + - - +
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Residues in contact with LEU 754 (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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625B LEU* 4.1 1.6 - - - -
626B VAL* 3.6 19.5 - - + +
634B LYS 6.0 1.1 - - - +
637B VAL* 4.5 10.5 - - + -
638B ALA* 4.2 13.5 - - + -
665B HIS* 4.9 9.2 - - + -
727B ILE* 3.9 23.8 - - + -
728B VAL 2.9 10.3 + - - +
729B ASP* 3.5 25.6 - - + +
730B GLU* 2.8 24.8 + - - -
731B GLU 4.3 0.2 + - - -
752B LEU* 4.2 17.9 - - + -
753B THR* 1.3 87.7 - - - +
755B THR* 1.3 65.9 + - - +
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Residues in contact with THR 755 (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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625B LEU* 4.0 17.9 - - + -
626B VAL 3.0 14.8 + - - +
627B CYS* 3.0 12.1 - - + +
628B GLY* 2.7 31.2 + - - +
729B ASP* 4.8 0.2 - - - -
730B GLU* 3.1 20.9 + - - -
731B GLU 6.0 0.2 - - - -
732B HIS* 4.3 4.2 - - - -
753B THR* 5.7 0.2 - - - -
754B LEU* 1.3 78.1 - - - +
756B ALA* 1.3 55.9 + - - +
757B THR* 3.5 25.4 + - - +
759B ILE* 5.4 3.1 - - + -
957B GLU* 4.2 7.1 + - - -
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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