Contacts of the strand formed by residues 722 - 734 (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 LEU 722 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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638B LEU* 5.1 2.5 - - + -
644B LYS* 4.8 6.1 - - + -
646B PHE* 3.7 30.7 - - + -
656B VAL* 4.6 6.5 - - + -
673B TYR* 3.2 50.0 + - + +
696B ILE* 3.8 26.0 - - + -
714B ALA* 4.2 10.8 - - + -
715B ARG 3.6 3.4 - - - +
716B VAL* 4.0 15.0 - - + -
720B GLY 4.1 8.3 - - - +
721B GLU* 1.3 89.2 - - - +
723B THR* 1.3 63.3 + - - +
724B TRP* 3.9 16.0 + - + +
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Residues in contact with THR 723 (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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714B ALA* 3.2 2.3 - - - -
715B ARG* 2.7 42.6 + - + -
717B GLU* 2.5 32.8 + - - +
721B GLU* 4.1 2.8 + - - +
722B LEU* 1.3 72.8 + - - +
724B TRP* 1.3 67.6 + - - +
725B LEU* 3.4 19.6 + - + +
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Residues in contact with TRP 724 (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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646B PHE* 4.5 3.6 - + - -
654B LEU* 3.6 20.2 - - + -
673B TYR* 3.4 44.1 - + + +
675B GLN* 3.6 40.1 + - + +
676B VAL* 3.7 15.9 - - + -
696B ILE* 4.5 5.2 - - + -
698B LEU* 4.0 23.8 - - + -
712B HIS* 3.3 32.5 - - + -
713B LEU 3.3 22.7 - - - -
714B ALA* 3.5 27.1 - - + -
722B LEU* 3.9 19.9 + - + +
723B THR* 1.3 77.2 - - - +
725B LEU* 1.3 60.9 + - - +
727B HIS* 3.7 8.5 - - - +
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Residues in contact with LEU 725 (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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675B GLN* 4.9 1.9 + - - -
695B TYR* 3.9 17.5 - - + -
713B LEU* 2.8 37.0 + - + +
715B ARG* 3.8 24.2 - - + +
723B THR* 3.6 28.7 - - + +
724B TRP* 1.3 73.9 - - - +
726B LYS* 1.3 79.2 + - + +
727B HIS* 4.9 6.5 + - - -
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Residues in contact with LYS 726 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
711B VAL 3.9 0.8 - - - +
712B HIS* 3.4 0.7 - - - -
713B LEU* 2.8 40.5 + - + +
725B LEU* 1.3 98.7 - - + +
727B HIS* 1.3 71.1 + - - +
728B ASN* 4.1 6.7 - - - +
774B LEU 3.2 27.8 - - - +
775B SER* 3.2 29.1 + - - +
776B LYS 4.4 8.1 - - - +
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Residues in contact with HIS 727 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
675B GLN* 3.0 58.6 + - - +
676B VAL* 4.3 0.8 - - - +
710B MET* 3.5 25.8 - - + +
711B VAL 3.6 4.5 - - - -
712B HIS* 3.0 33.0 - + + +
724B TRP* 3.7 17.6 - + + +
725B LEU 4.9 4.0 + - - -
726B LYS* 1.3 87.9 - - - +
728B ASN* 1.3 65.3 + - - +
729B PRO* 3.7 4.7 - - - +
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Residues in contact with ASN 728 (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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710B MET* 4.0 3.3 - - - +
711B VAL* 2.8 45.8 + - + +
726B LYS* 4.2 1.3 - - - +
727B HIS* 1.3 85.1 + - - +
729B PRO* 1.4 66.5 - - + +
730B ILE 3.6 0.2 + - - -
773B PHE* 2.5 45.5 + - + +
774B LEU* 2.8 26.0 + - + +
776B LYS* 3.5 33.2 - - + +
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Residues in contact with PRO 729 (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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308B LEU* 4.9 0.9 - - - +
708B ASN* 3.9 17.9 - - - +
709B GLY 3.3 8.7 - - - +
710B MET* 3.7 17.0 - - + -
727B HIS 3.7 7.9 - - - +
728B ASN* 1.4 84.0 - - + +
730B ILE* 1.3 58.9 + - - +
731B GLN 5.0 0.7 - - - +
732B LYS* 6.5 0.9 - - + -
773B PHE* 3.0 22.2 - - - -
776B LYS* 3.7 19.1 + - - +
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Residues in contact with ILE 730 (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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308B LEU* 3.8 28.7 - - + +
709B GLY* 2.7 26.4 + - - +
710B MET 4.6 0.2 - - - -
711B VAL* 3.7 32.1 - - + -
729B PRO* 1.3 75.6 - - - +
731B GLN* 1.3 63.8 + - + +
735B PHE* 4.3 15.5 - - + -
750B ILE* 3.8 22.0 - - + -
752B TYR* 5.2 2.4 - - + -
767B ARG* 3.4 25.3 + - - -
769B PHE* 3.7 26.9 - - + -
773B PHE* 4.1 5.4 - - + -
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Residues in contact with GLN 731 (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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311B LYS* 3.9 3.4 - - - +
708B ASN* 3.2 10.9 + - - -
709B GLY 2.9 26.8 + - - -
729B PRO* 3.8 1.6 - - - +
730B ILE* 1.3 82.4 - - + +
732B LYS* 1.3 89.6 + - - +
733B GLY 4.0 0.2 - - - +
734B GLU 4.1 6.1 - - - +
735B PHE* 3.8 19.7 - - + -
752B TYR* 2.8 37.9 + - + -
754B HIS* 3.3 35.5 + - - +
756B GLU* 4.9 2.0 + - - -
767B ARG* 3.3 17.1 + - - +
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Residues in contact with LYS 732 (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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708B ASN* 4.7 12.3 - - - +
729B PRO* 6.5 0.7 - - + -
731B GLN* 1.3 101.5 + - - +
733B GLY* 1.3 65.4 + - - +
754B HIS* 3.3 5.9 - - - -
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Residues in contact with GLY 733 (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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707B GLU* 4.1 10.7 - - - +
708B ASN* 3.0 25.1 + - - +
732B LYS* 1.3 77.7 - - - +
734B GLU* 1.3 66.1 - - - +
735B PHE* 4.0 1.2 - - - +
754B HIS* 4.5 3.6 - - - -
755B THR 5.6 0.2 - - - -
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Residues in contact with GLU 734 (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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705B LYS* 6.1 0.5 - - - +
706B ARG* 3.4 15.5 - - - +
707B GLU* 4.6 4.3 - - - +
731B GLN* 4.1 1.2 - - - +
733B GLY* 1.3 70.0 - - - +
735B PHE* 1.3 60.1 + - - +
753B GLU 4.2 1.3 - - - -
754B HIS* 2.6 35.3 + - - +
755B THR* 3.1 41.9 + - - +
762B TYR* 4.4 15.9 + - + -
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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