Contacts of the strand formed by residues 704 - 710 (chain A) in PDB entry 2PDA
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 ILE 704 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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695A CYS* 3.6 38.6 - - + +
696A ALA* 3.5 29.1 - - + +
699A CYS* 4.0 2.9 - - + +
702A SER* 3.4 10.6 + - - +
703A ALA* 1.3 77.4 - - - +
705A LEU* 1.3 64.4 + - - +
706A PRO* 3.8 1.1 - - - +
738A ILE* 3.9 21.3 - - + -
739A GLN 3.7 3.1 - - - -
740A ILE* 3.4 21.5 - - + -
751A CYS* 3.2 42.2 - - + -
762A LEU* 4.3 2.2 - - + -
822A ARG* 5.7 0.9 + - - -
1234A SF4 3.6 13.2 - - - -
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Residues in contact with LEU 705 (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 SER 5.6 2.0 - - - +
703A ALA 5.4 1.1 - - - +
704A ILE* 1.3 75.3 - - - +
706A PRO* 1.4 77.5 - - + +
707A VAL* 3.3 7.1 + - + -
739A GLN* 2.9 40.1 + - + +
741A ASN* 6.1 0.7 - - + -
778A LEU* 4.0 24.7 - - + -
781A ALA* 4.0 30.7 - - + +
782A ALA* 4.4 5.6 - - + +
786A VAL* 5.3 13.9 - - + -
804A PRO* 6.3 4.5 - - + -
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Residues in contact with PRO 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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693A ASN* 3.6 24.5 - - - +
696A ALA* 3.8 14.8 - - + -
704A ILE* 3.8 8.0 - - + +
705A LEU* 1.4 92.6 - - + +
707A VAL* 1.3 61.8 + - - +
736A PHE* 4.3 3.6 - - + -
737A ARG 3.5 6.3 - - - +
738A ILE* 4.6 6.3 - - + -
800A GLN* 2.8 37.6 - - + +
801A PHE* 3.3 21.9 - - + -
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Residues in contact with VAL 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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705A LEU* 4.0 13.2 - - + +
706A PRO* 1.3 74.0 - - - +
708A LEU* 1.3 64.5 + - - +
709A ALA* 4.0 22.7 - - + +
714A LEU* 4.9 1.3 - - + -
721A PHE* 4.4 19.7 - - + -
735A LYS 4.4 3.8 - - - +
736A PHE* 3.0 9.7 - - - -
737A ARG* 2.7 48.3 + - + +
739A GLN* 4.5 2.7 - - + -
781A ALA* 3.7 39.3 - - + +
784A ILE* 4.5 9.2 - - + -
801A PHE* 4.1 0.4 - - - -
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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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706A PRO 4.1 1.4 + - - -
707A VAL* 1.3 74.2 - - - +
709A ALA* 1.3 53.2 + - - +
726A ALA* 3.9 20.0 - - + -
731A LEU* 3.5 22.9 - - + -
734A TYR* 3.5 45.1 - - + -
735A LYS 3.5 2.2 - - - -
736A PHE* 4.1 15.0 - - + -
784A ILE* 4.9 0.3 - - - +
785A PRO 4.1 2.7 + - - +
787A LYS* 2.5 51.6 + - + +
790A VAL* 4.0 9.4 - - + -
801A PHE* 3.6 26.0 - - + -
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Residues in contact with ALA 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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707A VAL* 4.0 10.8 - - + -
708A LEU* 1.3 77.7 - - - +
710A LYS* 1.3 63.6 + - - +
711A GLU 3.5 0.9 + - - -
713A GLU* 3.0 17.9 - - - +
714A LEU* 3.2 34.0 - - + +
734A TYR* 3.9 3.6 - - - -
735A LYS* 2.8 32.5 + - - +
784A ILE* 4.0 7.0 - - + -
787A LYS* 3.7 0.7 - - - +
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Residues in contact with LYS 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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709A ALA* 1.3 74.7 - - - +
711A GLU* 1.3 62.1 + - + +
712A GLU* 3.0 11.8 + - + +
713A GLU* 2.6 56.8 + - + +
714A LEU 4.1 0.5 + - - -
733A GLY 3.5 15.5 - - - +
734A TYR* 3.4 42.7 + - + -
787A LYS* 4.0 10.5 - - - +
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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