Contacts of the strand formed by residues 738 - 742 (chain B) in PDB entry 2YA6
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 ASN 738 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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334B PRO* 3.8 3.7 - - - +
682B GLN* 3.0 36.1 + - - +
684B SER* 2.8 32.6 + - - -
699B SER* 3.0 43.3 + - - +
700B ASN* 3.6 3.8 - - - +
735B PHE* 3.5 12.3 - - + -
736B ALA 3.5 13.5 + - - -
737B TYR* 1.3 76.0 - - - +
739B SER* 1.3 61.3 + - - +
750B ILE* 4.2 5.8 - - + +
751B LEU 3.1 11.2 - - - +
752B TYR* 3.7 13.2 - - + -
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Residues in contact with SER 739 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334B PRO 3.7 17.3 - - - -
335B ALA* 3.7 1.4 - - - -
336B LEU* 2.9 44.5 + - - +
556B GLY* 4.3 3.3 - - - -
557B THR* 3.1 19.9 + - - -
684B SER* 3.4 5.7 - - - -
738B ASN* 1.3 76.8 - - - +
740B LEU* 1.3 60.9 + - - +
750B ILE* 4.4 1.3 - - - -
751B LEU 2.8 31.2 + - - -
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Residues in contact with LEU 740 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
557B THR* 5.1 1.2 - - - -
684B SER* 3.0 21.9 + - - +
686B ILE* 3.5 24.7 - - + +
697B ILE* 3.5 34.5 - - + +
699B SER* 3.5 34.5 - - - +
711B VAL* 5.0 0.9 - - + -
739B SER* 1.3 75.6 + - - +
741B GLN* 1.3 78.7 + - - +
748B TYR* 5.3 0.4 - - + -
749B GLY 3.4 4.9 - - - +
750B ILE* 3.8 25.1 - - + -
769B PHE* 3.7 30.1 - - + -
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Residues in contact with GLN 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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336B LEU* 2.9 48.7 + - + +
337B LEU* 3.7 8.3 - - - +
338B LYS* 3.0 33.0 + - + +
344B LEU* 5.0 4.3 - - + -
557B THR* 3.6 17.3 - - - +
686B ILE* 3.5 20.6 - - - +
740B LEU* 1.3 88.0 + - - +
742B GLU* 1.3 67.4 + - - +
743B LEU* 5.0 2.0 - - + -
748B TYR* 3.4 9.9 - - - +
749B GLY 2.9 29.1 + - - -
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Residues in contact with GLU 742 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338B LYS* 3.7 25.3 - - - +
686B ILE* 3.7 7.8 - - + +
687B HIS 4.1 13.5 - - - +
688B THR* 2.4 35.9 + - - +
689B MET 3.7 7.1 + - - +
741B GLN* 1.3 74.1 - - - +
743B LEU* 1.3 61.7 + - - +
744B GLY* 3.7 9.2 + - - +
747B GLU 4.9 0.2 - - - +
748B TYR* 3.3 24.0 - - + -
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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