Contacts of the strand formed by residues 788 - 796 (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 THR 788 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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714A LYS* 4.1 37.5 + - + +
715A TYR 3.5 4.5 - - - +
782A ILE* 3.5 5.4 - - + +
785A LEU* 3.3 27.9 + - + +
786A ASP 3.0 13.7 + - - -
787A ASN* 1.3 76.8 + - - +
789A GLU* 1.3 71.3 - - - +
790A ILE* 4.2 11.4 - - + -
868A ARG* 3.4 1.6 - - - -
869A ARG 2.9 28.9 + - - -
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Residues in contact with GLU 789 (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* 3.3 5.4 - - - -
715A TYR* 2.9 44.5 + - + +
716A GLY 5.2 4.8 - - - +
717A VAL* 5.5 0.2 - - - +
724A SER* 4.0 5.5 + - - -
729A PHE* 3.3 22.8 - - - -
788A THR* 1.3 78.2 - - - +
790A ILE* 1.3 61.3 + - - +
791A VAL 3.8 0.7 + - - -
865A MET* 3.5 30.6 - - + +
867A ASP 3.4 6.7 - - - +
868A ARG* 2.8 53.4 + - + +
870A LEU* 4.0 13.7 - - + +
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Residues in contact with ILE 790 (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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712A PHE* 4.2 24.2 - - + -
713A LEU 3.5 9.6 - - - +
714A LYS* 5.4 5.6 - - + -
738A VAL* 5.3 5.2 - - + -
762A SER* 3.5 33.9 - - - +
763A VAL* 4.3 8.3 - - + -
780A VAL* 4.7 9.0 - - + -
782A ILE* 3.6 31.9 - - + -
785A LEU* 5.0 2.7 - - + -
788A THR* 4.3 9.9 - - + -
789A GLU* 1.3 74.0 - - - +
791A VAL* 1.3 55.0 + - - +
865A MET* 3.3 4.6 - - - +
866A GLN* 2.8 45.2 + - + -
867A ASP 3.0 10.4 + - - +
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Residues in contact with VAL 791 (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 0.2 - - - +
712A PHE* 3.4 10.7 - - - -
713A LEU* 2.9 66.0 + - + +
715A TYR* 4.0 17.0 - - + -
735A ALA* 4.3 2.0 - - + -
789A GLU 3.8 0.6 + - - -
790A ILE* 1.3 74.4 - - - +
792A MET* 1.3 63.0 + - - +
793A ARG* 4.9 0.7 - - + +
828A TYR* 3.5 22.7 - - - +
863A GLU* 3.6 26.7 - - + +
864A ILE 3.6 14.1 - - - +
865A MET* 3.7 11.0 - - - +
866A GLN* 4.6 0.2 - - - -
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Residues in contact with MET 792 (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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710A PHE* 3.5 42.4 - - + -
711A LYS 3.7 4.5 - - - +
712A PHE* 3.7 25.1 - - + -
765A HIS* 4.4 4.0 - - - -
776A ILE* 4.6 1.8 - - - -
778A ASN* 3.3 21.3 - - - +
791A VAL* 1.3 73.5 - - - +
793A ARG* 1.3 59.9 + - - +
846A LEU* 4.3 7.0 - - + -
863A GLU* 3.2 2.3 - - - -
864A ILE* 2.8 59.3 + - + +
866A GLN* 3.8 11.5 - - - +
892A TYR* 3.9 29.4 - - + -
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Residues in contact with ARG 793 (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 HIS 3.5 0.7 - - - +
710A PHE* 3.4 7.7 - - - -
711A LYS* 2.8 35.5 + - + +
713A LEU* 3.6 43.7 - - + +
715A TYR* 4.0 10.1 + - - -
734A PRO* 6.0 1.0 - - - +
735A ALA* 4.1 19.8 + - - +
791A VAL* 4.0 2.3 - - + +
792A MET* 1.3 74.0 - - - +
794A LEU* 1.3 74.6 + - - +
795A GLU* 4.2 18.2 + - + -
857A LEU* 4.6 5.3 - - - +
861A GLU* 3.6 31.2 + - - +
862A LEU 3.3 11.7 - - - +
863A GLU* 2.9 34.9 + - + -
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Residues in contact with LEU 794 (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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708A VAL* 3.7 28.0 - - + -
709A HIS 3.3 5.2 - - - +
710A PHE* 3.4 46.0 - - + -
793A ARG* 1.3 72.9 - - - +
795A GLU* 1.3 59.0 + - - +
796A THR* 5.0 0.9 - - + -
844A LEU* 4.1 15.7 - - + -
846A LEU* 4.5 13.5 - - + -
860A GLY 3.9 0.6 - - - +
861A GLU* 3.2 10.2 - - - +
862A LEU* 2.7 50.0 + - + +
894A LEU* 3.7 25.4 - - + -
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Residues in contact with GLU 795 (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 PRO* 4.0 1.0 - - - +
708A VAL* 3.6 1.7 - - - -
709A HIS* 2.9 54.2 + - + +
711A LYS* 2.9 47.7 + - + +
793A ARG* 4.2 23.1 + - + -
794A LEU* 1.3 74.4 - - - +
796A THR* 1.3 65.3 + - - +
797A HIS* 5.5 1.6 - - + -
860A GLY 4.1 1.1 - - - -
861A GLU* 4.5 14.9 - - + +
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Residues in contact with THR 796 (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 VAL* 6.0 1.3 - - - -
707A PRO* 3.6 17.5 - - - +
708A VAL* 4.4 9.9 - - + -
794A LEU 4.8 0.9 - - - -
795A GLU* 1.3 82.6 - - - +
797A HIS* 1.3 75.7 - - - +
798A ILE* 3.0 34.9 + - + +
837A ILE* 3.9 1.3 - - + +
844A LEU* 3.7 29.6 - - + -
859A SER 4.4 2.8 - - - +
860A GLY* 2.7 34.1 + - - +
861A GLU* 5.8 0.3 - - - +
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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