Contacts of the strand formed by residues 705 - 713 (chain A) in PDB entry 5L73
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 VAL 705 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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669A VAL* 2.9 48.5 - - + +
670A GLN 4.2 1.1 + - - +
671A LEU* 3.5 16.2 + - - -
703A GLY 4.0 9.0 - - - +
704A LYS* 1.3 80.9 - - - +
706A ALA* 1.3 59.8 + - - +
707A ARG* 4.1 21.1 - - + +
737A ARG* 4.9 0.2 - - - +
782A GLU* 4.0 22.0 - - + +
783A GLY 3.2 7.2 - - - +
784A GLU* 4.1 20.4 - - + +
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Residues in contact with ALA 706 (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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671A LEU* 3.5 12.6 - - + +
672A LYS* 3.5 36.3 - - - +
673A TRP* 3.5 15.6 + - + +
695A SER* 4.1 12.1 - - - +
705A VAL* 1.3 73.2 - - - +
707A ARG* 1.3 60.0 + - - +
782A GLU* 3.3 5.2 - - - +
783A GLY 2.8 32.6 + - - +
785A ILE* 5.4 2.0 - - + +
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Residues in contact with ARG 707 (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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665A HIS* 3.6 5.2 + - - +
666A ASP* 2.9 54.8 + - + +
668A HIS* 6.1 1.4 - - - +
669A VAL* 3.4 31.7 - - + +
671A LEU 4.4 1.0 + - - -
672A LYS* 5.4 0.6 - - - +
673A TRP* 4.1 2.9 - - - -
705A VAL* 4.1 10.0 - - + +
706A ALA* 1.3 77.2 - - - +
708A LEU* 1.3 60.5 + - - +
709A VAL* 4.9 0.4 - - + -
739A LYS* 3.5 13.8 - - - +
741A ARG* 4.1 21.3 - - - +
749A ASP* 5.3 1.5 + - - -
780A ILE* 3.7 23.0 - - + +
781A PHE 3.6 2.5 - - - -
782A GLU* 2.6 31.6 + - + +
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Residues in contact with LEU 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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652A PHE* 4.2 8.7 - - + -
660A PHE* 3.8 33.2 - - + -
663A TRP* 3.7 37.3 - - + -
664A GLU 3.5 14.4 - - - +
665A HIS* 3.9 22.2 - - + +
673A TRP* 3.8 15.2 - - + +
693A ILE* 4.1 21.1 - - + -
707A ARG* 1.3 73.7 - - - +
709A VAL* 1.3 60.5 + - - +
780A ILE* 3.3 5.2 - - - -
781A PHE* 2.9 39.6 + - + +
798A ILE* 5.4 0.9 - - + -
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Residues in contact with VAL 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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662A HIS 4.3 0.3 - - - +
663A TRP* 3.3 3.6 - - - -
664A GLU* 2.7 50.3 + - + +
665A HIS 4.7 0.2 - - - -
666A ASP* 4.1 26.0 - - + +
707A ARG 4.2 1.6 - - - +
708A LEU* 1.3 76.5 - - - +
710A SER* 1.3 65.2 + - - +
741A ARG* 4.5 17.9 - - - +
778A GLN* 3.8 35.7 - - + +
779A VAL 3.6 3.6 - - - +
780A ILE* 4.5 13.9 - - + +
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Residues in contact with SER 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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648A PHE* 3.6 10.1 - - - -
662A HIS 4.5 1.1 - - - -
663A TRP* 3.4 31.0 - - - -
664A GLU* 6.2 0.2 - - - -
709A VAL* 1.3 74.8 - - - +
711A PRO* 1.3 91.1 + - - +
778A GLN* 2.9 25.8 + - - +
779A VAL 2.7 39.0 + - - -
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Residues in contact with PRO 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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643A PHE* 6.1 1.6 - - + -
646A TYR 5.4 1.6 - - - +
647A GLY* 3.9 11.9 - - - +
648A PHE* 3.9 20.0 - - + +
662A HIS* 3.7 38.5 - - + +
663A TRP* 4.1 11.4 - - + +
710A SER* 1.3 107.9 + - - +
712A VAL* 1.3 69.6 + - - +
713A VAL 3.4 2.3 + - - -
778A GLN* 3.9 2.9 - - - +
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Residues in contact with VAL 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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643A PHE* 4.2 8.8 - - - -
710A SER 3.8 0.2 + - - -
711A PRO* 1.3 76.7 - - - +
713A VAL* 1.3 74.0 + - - +
714A TYR* 3.8 31.1 + - + +
743A GLN* 4.4 19.5 - - + +
776A LEU* 4.0 29.6 - - + -
777A TYR 3.7 10.1 - - - +
778A GLN* 3.8 20.2 - - + +
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Residues in contact with VAL 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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643A PHE* 3.9 17.0 - - + -
648A PHE* 3.8 29.8 - - + -
710A SER* 4.5 0.4 - - - +
711A PRO 4.2 2.0 - - - +
712A VAL* 1.3 83.0 - - - +
714A TYR* 1.3 69.4 + - - +
715A SER* 3.4 17.3 + - - -
720A HIS* 4.2 10.5 - - - +
770A LEU* 4.2 9.6 - - + -
776A LEU* 3.9 5.9 - - - +
777A TYR* 2.9 49.0 + - + +
779A VAL* 4.1 11.4 - - + -
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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