Contacts of the strand formed by residues 738 - 744 (chain B) in PDB entry 2X2M
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 738 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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729B THR* 3.8 1.6 - - - +
730B LEU* 2.8 29.5 + - + -
731B GLY* 2.8 21.4 + - - +
737B LYS* 1.3 80.5 - - - +
739B VAL* 1.3 68.7 + - - +
756B ALA* 4.0 24.2 - - + -
757B VAL 3.3 9.6 - - - +
758B LYS* 3.6 29.6 - - + -
892B ASP* 5.8 0.2 - - - +
2015B X2M 4.0 30.5 - - + -
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Residues in contact with VAL 739 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
726B LEU* 4.2 16.6 - - + -
727B GLY 3.9 6.7 - - - +
728B LYS 3.4 10.1 - - - +
729B THR* 4.0 19.1 - - - +
730B LEU* 3.9 5.4 - - - -
737B LYS* 4.3 13.7 - - + +
738B VAL* 1.3 79.9 - - - +
740B LYS* 1.3 73.2 + - - +
756B ALA* 3.3 3.6 - - - -
757B VAL* 2.8 54.8 + - + -
759B MET* 3.9 23.3 - - + -
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Residues in contact with LYS 740 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
727B GLY* 2.8 31.8 + - - -
728B LYS* 2.9 40.4 + - + +
730B LEU* 3.5 16.4 - - + +
739B VAL* 1.3 76.5 - - - +
741B ALA* 1.3 58.2 + - - +
754B THR* 3.8 18.6 - - + +
755B VAL 3.8 6.3 - - - +
806B TYR* 3.1 46.3 + - + +
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Residues in contact with ALA 741 (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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724B LEU* 4.0 5.8 - - + -
725B VAL 3.2 15.3 - - - +
726B LEU* 4.1 7.2 - - + -
727B GLY* 4.2 1.1 - - - +
739B VAL 4.3 0.4 - - - +
740B LYS* 1.3 78.6 - - - +
742B THR* 1.3 62.7 + - - +
754B THR* 3.6 8.1 + - - +
755B VAL* 2.9 35.1 + - + +
757B VAL* 3.5 31.2 - - + -
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Residues in contact with THR 742 (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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723B ASN 3.9 0.7 - - - +
724B LEU* 3.5 5.3 - - - +
725B VAL* 2.9 57.0 + - + +
741B ALA* 1.3 75.6 - - - +
743B ALA* 1.3 60.9 + - - +
752B TYR* 3.5 35.8 - - + +
753B THR 3.4 13.1 + - - -
754B THR* 4.3 5.9 + - - -
755B VAL* 4.3 0.4 - - - -
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Residues in contact with ALA 743 (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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719B PHE* 3.9 20.4 - - + -
723B ASN 3.4 3.6 - - - -
724B LEU* 4.2 9.2 - - + -
742B THR* 1.3 77.1 + - - +
744B PHE* 1.3 61.1 + - - +
745B HIS 3.7 0.3 + - - -
746B LEU* 4.1 26.5 - - + +
751B GLY 3.5 1.6 - - - +
752B TYR* 3.4 4.1 - - - -
753B THR* 2.9 38.2 + - - +
755B VAL* 4.3 5.4 - - + -
803B ILE* 4.9 1.1 - - + -
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Residues in contact with PHE 744 (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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719B PHE* 3.4 13.9 - - - -
723B ASN* 2.7 44.5 + - + +
743B ALA* 1.3 71.1 - - - +
745B HIS* 1.3 82.4 + + + +
751B GLY* 3.4 26.5 - - - -
752B TYR* 3.7 41.2 - + + +
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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