Contacts of the strand formed by residues 738 - 744 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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334A PRO* 3.7 5.1 - - - +
682A GLN* 3.0 34.0 + - - -
683A MET* 4.0 3.2 - - - +
684A SER* 2.7 31.5 + - - -
699A SER* 3.0 45.2 + - - +
700A ASN* 3.9 5.3 - - - +
735A PHE* 4.0 3.9 - - + -
736A ALA 3.5 12.5 + - - -
737A TYR* 1.3 74.4 - - - +
739A SER* 1.3 61.8 + - - +
750A ILE* 4.0 9.7 - - + +
751A LEU 3.1 13.2 - - - +
752A TYR* 3.7 12.3 - - + -
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Residues in contact with SER 739 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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334A PRO* 3.8 16.2 - - - -
335A ALA* 3.7 2.3 - - - -
336A LEU* 2.9 39.0 + - - +
556A GLY* 4.2 3.3 - - - -
557A THR* 3.0 21.7 + - - -
684A SER* 3.4 6.4 - - - -
738A ASN* 1.3 78.1 - - - +
740A LEU* 1.3 60.8 + - - +
750A ILE* 3.4 4.4 - - - -
751A LEU 2.8 32.5 + - - -
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Residues in contact with LEU 740 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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557A THR* 4.9 1.7 + - - -
684A SER* 3.0 33.2 + - - +
685A ALA* 4.3 0.4 - - - -
686A ILE* 3.4 25.3 - - + +
697A ILE* 3.5 39.7 - - + +
699A SER* 3.9 16.2 - - - +
711A VAL* 5.1 0.4 - - + -
739A SER* 1.3 76.7 + - - +
741A GLN* 1.3 79.1 + - - +
748A TYR* 5.2 1.6 - - + -
749A GLY 3.5 10.8 - - - +
750A ILE* 4.1 16.2 - - + -
769A PHE* 3.9 28.7 - - + -
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Residues in contact with GLN 741 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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336A LEU* 3.0 50.7 + - + +
337A LEU* 3.5 5.1 - - - +
338A LYS* 2.9 28.8 + - + +
344A LEU* 4.9 0.2 - - + -
557A THR* 4.0 13.3 - - - +
686A ILE* 3.7 17.3 - - - +
740A LEU* 1.3 88.6 + - - +
742A GLU* 1.3 63.0 + - - +
743A LEU* 4.0 8.7 - - + +
748A TYR* 3.4 5.4 - - - +
749A GLY 2.9 32.9 + - - +
1781A FMT 2.9 28.5 + - - +
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Residues in contact with GLU 742 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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338A LYS* 4.1 19.2 - - - +
686A ILE* 3.7 9.1 - - + +
687A HIS 4.1 11.8 - - - +
688A THR* 2.6 30.3 + - - -
689A MET 4.0 4.7 + - - +
741A GLN* 1.3 73.8 - - - +
743A LEU* 1.3 63.8 + - - +
744A GLY* 4.3 9.9 - - - +
747A GLU 4.5 0.4 - - - +
748A TYR* 3.6 23.9 + - + -
1781A FMT 4.5 10.0 + - - +
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Residues in contact with LEU 743 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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338A LYS* 3.1 28.1 + - + +
344A LEU* 3.7 31.6 - - + -
371A ASN* 3.6 23.1 + - - +
741A GLN* 4.0 9.2 - - + +
742A GLU* 1.3 77.0 - - - +
744A GLY* 1.3 61.3 + - - +
747A GLU* 2.8 16.2 + - + +
748A TYR* 3.6 11.7 - - - +
749A GLY* 3.4 21.8 - - - +
766A PHE* 4.3 3.8 - - + -
768A LYS* 3.3 42.2 - - + -
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Residues in contact with GLY 744 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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742A GLU* 3.5 10.4 - - - +
743A LEU* 1.3 81.7 - - - +
745A ASN* 1.3 75.4 + - - +
746A GLY 3.3 2.9 - - - -
747A GLU* 3.1 19.9 + - - +
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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