Contacts of the strand formed by residues 705 - 715 (chain A) in PDB entry 1QWN
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 HIS 705 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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677A SER* 5.6 1.8 - - - -
685A THR* 4.7 12.6 + - + -
687A ALA* 5.3 4.7 - - + +
696A SER* 3.8 24.8 + - - +
697A ILE 3.9 4.9 - - - -
698A GLN* 3.4 42.8 + - + +
703A SER 4.8 0.9 - - - -
704A PRO* 1.3 73.8 - - + +
706A VAL* 1.3 62.6 + - - +
707A PRO* 3.5 9.5 - - - +
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Residues in contact with VAL 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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696A SER* 3.1 3.1 - - - -
697A ILE 3.0 38.4 + - - +
699A LEU* 5.8 3.6 - - + -
704A PRO* 3.7 21.3 - - + +
705A HIS* 1.3 70.5 - - - +
707A PRO* 1.3 80.6 - - + +
708A VAL* 3.1 6.2 + - + +
796A THR* 6.0 1.1 - - - -
797A HIS 6.3 0.2 - - - +
798A ILE* 6.0 3.4 - - + -
842A THR* 5.0 9.0 - - + -
896A LEU* 3.8 30.3 - - + -
898A LYS* 6.3 2.9 - - + -
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Residues in contact with PRO 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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695A LYS 3.6 8.3 - - - +
696A SER* 4.5 1.8 - - - -
705A HIS 3.5 9.2 - - - +
706A VAL* 1.3 86.9 - - + +
708A VAL* 1.3 65.9 + - - +
709A HIS* 4.0 17.7 - - + +
795A GLU 4.3 1.3 - - - -
796A THR* 3.6 18.6 - - - -
797A HIS* 4.0 40.4 + - + +
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Residues in contact with VAL 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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694A LEU* 3.3 27.5 - - + +
695A LYS* 3.0 25.0 + - - -
696A SER* 4.7 0.4 - - - -
697A ILE* 4.3 18.4 - - + -
706A VAL* 3.1 22.3 + - + +
707A PRO* 1.3 80.4 - - - +
709A HIS* 1.3 60.0 + - - +
794A LEU* 3.7 25.4 - - + -
795A GLU 3.6 3.8 - - - -
796A THR* 4.4 8.3 - - + -
844A LEU* 4.1 15.0 - - + -
894A LEU* 4.3 5.6 - - + -
896A LEU* 4.5 12.1 - - + -
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Residues in contact with HIS 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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694A LEU 3.2 5.2 - - - +
695A LYS* 3.0 56.1 + - + +
707A PRO* 4.0 18.6 - - + +
708A VAL* 1.3 80.2 + - - +
710A PHE* 1.3 63.9 + - - +
711A LYS* 3.9 0.4 + - + -
793A ARG 3.5 0.9 - - - +
794A LEU* 3.3 7.7 - - - -
795A GLU* 2.9 60.4 + - + +
797A HIS* 6.2 1.1 - + - -
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Residues in contact with PHE 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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693A LEU* 3.8 37.2 - - + +
694A LEU* 3.2 31.9 + - + +
708A VAL 4.2 0.4 + - - -
709A HIS* 1.3 76.3 - - - +
711A LYS* 1.3 60.3 + - - +
712A PHE* 5.3 1.1 - - + -
765A HIS* 3.9 16.6 - + + +
767A THR* 5.2 0.7 - - - -
776A ILE* 3.7 37.0 - - + -
792A MET* 3.5 44.2 - - + -
793A ARG 3.4 2.2 - - - -
794A LEU* 3.4 39.3 - - + -
846A LEU* 4.8 2.9 - - + -
894A LEU* 3.8 18.6 - - + -
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Residues in contact with LYS 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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693A LEU* 5.0 4.0 - - - -
709A HIS* 6.0 0.2 - - + -
710A PHE* 1.3 77.1 - - - +
712A PHE* 1.3 72.6 + - - +
713A LEU* 3.9 30.1 - - + -
737A PRO* 4.9 12.7 - - + +
792A MET* 3.7 2.8 - - - +
793A ARG* 2.8 38.9 + - + +
795A GLU* 2.9 43.2 + - - +
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Residues in contact with PHE 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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693A LEU* 4.0 14.2 - - + +
710A PHE* 5.3 1.3 - - + -
711A LYS* 1.3 79.9 - - - +
713A LEU* 1.3 63.2 + - - +
737A PRO* 3.8 1.9 - - - +
738A VAL* 3.0 37.0 + - + +
740A LEU* 5.3 6.3 - - + +
760A LEU* 3.7 25.4 - - + -
763A VAL* 4.1 19.5 - - + -
765A HIS* 3.6 37.9 - + - -
778A ASN* 3.8 19.3 - - - -
790A ILE* 4.2 14.1 - - + -
791A VAL 3.4 13.9 - - - -
792A MET* 3.7 27.6 - - + -
866A GLN* 4.5 4.5 - - + -
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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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711A LYS* 3.9 23.8 - - + +
712A PHE* 1.3 79.3 - - - +
714A LYS* 1.3 61.5 + - - +
735A ALA* 3.7 24.9 - - + +
736A SER 3.3 8.3 - - - +
737A PRO* 3.8 24.5 - - + -
738A VAL* 3.8 9.1 - - - +
790A ILE* 3.5 5.4 - - - +
791A VAL* 2.9 37.4 + - + +
793A ARG* 3.6 58.6 - - + +
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Residues in contact with LYS 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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713A LEU* 1.3 75.3 - - - +
715A TYR* 1.3 61.8 + - - +
716A GLY 4.3 0.2 + - - -
735A ALA* 3.3 6.4 - - - -
736A SER* 2.8 51.2 + - - +
737A PRO 4.7 2.7 - - - +
738A VAL* 3.8 31.5 - - + +
739A GLU 5.8 0.4 - - - +
761A PRO* 6.2 1.0 - - - +
785A LEU* 4.0 26.7 - - - +
788A THR* 4.1 20.5 + - + +
789A GLU 3.3 8.7 - - - +
790A ILE* 5.2 2.9 - - - -
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Residues in contact with TYR 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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714A LYS* 1.3 75.5 - - - +
716A GLY* 1.3 62.9 + - - +
729A PHE* 3.9 15.0 - + + -
731A PRO* 3.7 10.5 - - + -
733A GLY 3.5 21.8 - - - -
735A ALA* 3.4 33.4 + - + +
788A THR* 3.5 7.8 - - - +
789A GLU* 2.9 42.1 + - + +
791A VAL* 4.0 8.7 - - + -
793A ARG* 4.0 2.9 + - - -
824A LEU* 3.9 19.5 - - + +
828A TYR* 3.9 1.1 - - - -
857A LEU* 3.3 19.2 - - - +
863A GLU* 2.6 30.1 + - - -
865A MET* 3.6 33.4 - - + -
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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