Contacts of the strand formed by residues 707 - 716 (chain A) in PDB entry 2YA4
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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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701A ALA* 3.9 1.7 - - - +
702A GLY 3.2 13.5 + - - -
703A GLY 3.2 20.0 + - - +
704A PRO* 3.4 16.4 - - - +
705A LYS* 2.9 41.0 + - - +
706A ARG* 1.3 75.4 - - - +
708A ASN* 1.3 74.3 + - + +
709A GLY 3.7 0.7 - - - -
733A GLY* 3.0 20.0 - - - +
734A GLU* 4.5 2.7 - - - +
735A PHE* 3.6 6.9 + - - +
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Residues in contact with ASN 708 (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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702A GLY* 2.9 24.1 + - - +
703A GLY 4.2 12.0 + - - +
707A GLU* 1.3 75.1 - - + +
709A GLY* 1.3 64.2 + - - +
710A MET* 3.4 19.7 - - - +
729A PRO* 3.6 12.4 - - - +
731A GLN 3.3 7.8 - - - +
732A LYS* 3.2 33.4 - - + +
733A GLY 2.8 19.3 + - - +
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Residues in contact with GLY 709 (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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700A ASN 3.8 0.9 - - - -
708A ASN* 1.3 72.5 - - - +
710A MET* 1.3 54.8 + - - -
729A PRO* 3.1 6.9 - - - +
730A ILE* 2.7 35.2 + - - -
731A GLN 2.8 13.5 + - - -
735A PHE* 3.2 41.9 - - - +
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Residues in contact with MET 710 (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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699A SER* 2.8 32.1 + - - -
700A ASN 2.9 9.9 + - - +
702A GLY* 3.5 18.8 - - - -
708A ASN* 3.4 30.3 - - - +
709A GLY* 1.3 73.4 - - - +
711A VAL* 1.3 63.8 + - - +
712A HIS* 3.5 25.4 - - + +
727A HIS* 3.7 40.8 - - + +
728A ASN 3.5 1.8 - - - -
729A PRO* 3.6 26.0 - - + -
730A ILE* 4.2 0.2 - - - +
735A PHE* 4.5 0.4 - - - -
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Residues in contact with VAL 711 (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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697A ILE* 3.4 32.1 - - + -
698A LEU 3.7 2.5 - - - -
699A SER* 4.1 10.5 - - - +
710A MET* 1.3 80.0 - - - +
712A HIS* 1.3 59.4 + - - +
713A LEU 4.1 0.3 + - - -
726A LYS* 4.0 1.4 - - - +
727A HIS* 3.7 1.2 - - - -
728A ASN* 2.8 38.0 + - - +
730A ILE* 3.6 35.9 - - + -
740A LEU* 5.3 0.2 - - + -
750A ILE* 4.7 1.3 - - + -
769A PHE* 4.1 13.2 - - + -
773A PHE* 4.1 9.4 - - + -
774A LEU* 3.6 21.6 - - + +
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Residues in contact with HIS 712 (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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675A GLN 5.1 0.4 - - - -
676A VAL* 3.7 21.4 - - + +
677A LYS 5.1 3.3 + - - -
697A ILE* 3.4 7.1 - - - +
698A LEU* 2.7 59.5 + - + +
700A ASN* 2.6 29.9 + - - -
701A ALA 5.1 1.3 + - - -
702A GLY* 5.7 1.3 - - - -
710A MET* 3.5 33.8 - - + +
711A VAL* 1.3 75.3 - - - +
713A LEU* 1.3 61.0 + - - +
724A TRP* 3.5 24.6 - - + -
726A LYS 3.4 4.0 - - - -
727A HIS* 3.0 27.8 + - - +
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Residues in contact with LEU 713 (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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695A TYR* 3.9 25.6 - - + -
696A ILE 3.8 4.7 - - - +
697A ILE* 4.2 14.6 - - + -
711A VAL 4.1 0.6 + - - +
712A HIS* 1.3 72.8 - - - +
714A ALA* 1.3 60.9 - - - +
724A TRP* 3.5 6.2 - - - -
725A LEU* 2.9 35.6 + - + +
726A LYS* 2.9 42.5 + - + -
771A TRP* 3.9 39.9 - - + +
774A LEU* 4.4 24.0 - - + +
775A SER* 5.2 1.1 - - - +
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Residues in contact with ALA 714 (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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695A TYR* 3.2 12.7 - - - +
696A ILE* 2.9 41.0 + - + +
713A LEU* 1.3 73.3 - - - +
715A ARG* 1.3 61.4 + - - +
722A LEU* 4.2 13.7 - - + -
723A THR 3.2 9.4 - - - +
724A TRP* 3.3 39.2 - - + -
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Residues in contact with ARG 715 (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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693A LYS* 4.0 34.6 - - - +
694A GLU 3.2 21.7 + - - +
695A TYR* 3.6 20.3 + - + -
714A ALA* 1.3 73.9 - - - +
716A VAL* 1.3 76.5 + - - +
717A GLU* 3.6 31.2 + - - +
718A GLU 5.5 2.6 - - - +
722A LEU* 3.3 5.4 - - - -
723A THR* 2.8 38.9 + - - +
725A LEU* 3.9 19.8 - - + +
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Residues in contact with VAL 716 (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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638A LEU* 4.1 18.6 - - + -
694A GLU* 2.9 56.1 + - + +
695A TYR* 3.8 21.1 - - - -
696A ILE* 3.9 11.7 - - + +
715A ARG* 1.3 88.1 + - - +
717A GLU* 1.3 68.0 + - - +
718A GLU 4.0 0.3 + - - -
720A GLY* 4.9 0.9 - - - +
721A GLU 3.5 4.7 - - - +
722A LEU* 3.7 23.8 - - + -
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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