Contacts of the strand formed by residues 707 - 716 (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 GLU 707 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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701B ALA* 3.6 1.9 - - - +
702B GLY 3.1 6.4 + - - -
703B GLY 3.0 34.8 + - - +
704B PRO* 3.3 20.8 - - - +
705B LYS* 2.7 47.5 + - + +
706B ARG* 1.3 73.3 - - - +
708B ASN* 1.3 64.7 + - + +
709B GLY 3.8 0.4 - - - -
733B GLY* 3.4 21.0 - - - +
734B GLU* 4.5 4.3 - - - +
735B PHE* 3.4 8.8 + - - +
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Residues in contact with ASN 708 (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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702B GLY* 2.7 27.4 + - - +
703B GLY 4.1 12.1 - - - +
707B GLU* 1.3 76.0 - - + +
709B GLY* 1.3 64.4 + - - +
710B MET* 3.1 11.6 + - - +
729B PRO* 3.9 27.6 - - - +
731B GLN 3.2 16.5 + - - -
732B LYS* 4.7 11.0 - - - +
733B GLY 3.0 15.0 + - - +
735B PHE* 3.9 0.2 - - - +
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Residues in contact with GLY 709 (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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700B ASN 3.8 0.2 - - - -
708B ASN* 1.3 71.4 + - - +
710B MET* 1.3 57.6 + - - -
729B PRO* 3.3 5.2 - - - +
730B ILE* 2.7 37.0 + - - -
731B GLN 2.9 12.2 + - - -
735B PHE* 3.3 43.0 - - - +
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Residues in contact with MET 710 (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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698B LEU 3.9 1.0 - - - +
699B SER* 3.2 6.6 + - - -
700B ASN 2.7 36.1 + - - +
702B GLY* 3.5 19.1 - - - +
708B ASN* 3.4 19.5 - - - +
709B GLY* 1.3 73.9 - - - +
711B VAL* 1.3 61.0 + - - +
712B HIS* 3.6 24.1 + - + +
727B HIS* 3.5 43.3 - - + +
728B ASN 3.6 0.9 - - - -
729B PRO* 3.7 30.1 - - + -
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Residues in contact with VAL 711 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
697B ILE* 3.5 30.7 - - + -
698B LEU 3.7 3.4 - - - +
699B SER* 4.3 8.7 - - - +
710B MET* 1.3 75.1 - - - +
712B HIS* 1.3 60.3 + - - +
726B LYS 3.9 1.0 - - - +
727B HIS* 3.6 0.7 - - - -
728B ASN* 2.8 45.6 + - + +
730B ILE* 3.7 41.5 - - + -
740B LEU* 5.0 2.2 - - + -
750B ILE* 4.9 1.6 - - + -
769B PHE* 4.0 13.9 - - + -
773B PHE* 4.2 8.1 - - + -
774B LEU* 3.8 17.1 - - + +
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Residues in contact with HIS 712 (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 4.6 1.0 + - - -
676B VAL* 3.7 30.0 - - + +
677B LYS* 4.7 3.7 + - - +
697B ILE* 3.2 12.0 - - - +
698B LEU* 2.7 54.0 + - - +
700B ASN* 2.9 27.3 + - - -
701B ALA 5.5 0.9 - - - -
702B GLY* 6.0 0.4 - - - -
710B MET* 3.6 27.4 + - + +
711B VAL* 1.3 74.8 - - - +
713B LEU* 1.3 60.6 + - - +
724B TRP* 3.3 23.1 - - + -
726B LYS 3.4 3.6 - - - -
727B HIS* 3.0 37.0 - + + +
774B LEU* 5.0 0.4 - - - -
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Residues in contact with LEU 713 (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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695B TYR* 3.9 17.3 - - + -
696B ILE 3.7 4.3 - - - +
697B ILE* 4.4 11.0 - - + -
712B HIS* 1.3 74.0 - - - +
714B ALA* 1.3 62.7 + - - +
724B TRP* 3.3 8.0 - - - -
725B LEU* 2.8 54.0 + - + -
726B LYS* 2.8 27.8 + - + +
771B TRP* 3.7 42.0 - - + +
774B LEU* 4.3 28.5 - - + +
775B SER* 5.2 2.0 - - - +
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Residues in contact with ALA 714 (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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695B TYR* 3.3 12.7 - - - +
696B ILE* 2.9 37.7 + - + +
713B LEU* 1.3 75.1 - - - +
715B ARG* 1.3 64.0 + - - +
722B LEU* 4.2 14.4 - - + -
723B THR 3.2 12.1 - - - +
724B TRP* 3.5 33.6 - - + -
725B LEU* 4.3 0.9 - - - +
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Residues in contact with ARG 715 (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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692B GLY 5.4 0.4 + - - -
693B LYS* 3.8 29.0 - - - +
694B GLU* 3.0 41.3 + - - +
695B TYR* 3.7 18.5 + - - -
714B ALA* 1.3 73.8 - - - +
716B VAL* 1.3 80.5 + - - +
717B GLU* 3.7 16.8 + - - +
722B LEU* 3.6 3.5 - - - -
723B THR* 2.7 44.4 + - - +
725B LEU* 3.8 20.0 - - + +
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Residues in contact with VAL 716 (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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638B LEU* 4.1 22.0 - - + -
640B ASN* 5.9 0.9 - - - +
687B HIS* 5.3 0.2 - - + -
694B GLU* 3.0 52.9 + - + +
695B TYR 3.8 17.9 - - - +
696B ILE* 4.1 15.7 - - + +
714B ALA 4.7 0.2 - - - +
715B ARG* 1.3 96.1 + - - +
717B GLU* 1.3 71.8 + - - +
718B GLU 4.0 0.2 + - - -
721B GLU 3.5 4.0 - - - +
722B LEU* 4.0 13.0 - - + -
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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