Contacts of the strand formed by residues 811 - 820 (chain A) in PDB entry 3I7O
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 811 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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787A GLU 5.6 0.5 - - - +
789A HIS* 3.6 21.7 + - - +
807A PHE* 3.5 13.8 - - + +
808A LEU* 2.7 48.5 + - + +
809A GLN 3.1 0.6 + - - -
810A ASN* 1.3 76.3 - - - +
812A TYR* 1.3 69.8 + - - +
813A ALA 4.1 0.2 + - - -
833A THR* 3.2 20.7 + - + +
834A ALA 3.6 4.3 - - - +
835A MET* 3.6 17.3 - - - -
847A ARG* 2.4 47.6 + - - +
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Residues in contact with TYR 812 (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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786A VAL* 6.0 0.5 - - - +
787A GLU* 3.2 18.4 + - + +
789A HIS* 3.5 14.4 - + - -
810A ASN* 3.7 24.1 + - - -
811A GLU* 1.3 78.9 - - - +
813A ALA* 1.3 56.6 + - - +
814A LEU* 3.5 14.7 + - + +
833A THR* 2.7 36.5 - - - -
834A ALA* 2.8 17.6 + - + +
836A VAL* 3.8 21.8 - - + +
11B LEU* 5.3 0.7 - - + -
12B TRP* 2.6 42.1 - + - -
15B ARG* 2.2 55.2 - - - -
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Residues in contact with ALA 813 (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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722A ARG* 4.9 6.9 + - - +
736A LEU* 3.4 31.4 - - + +
789A HIS* 3.6 22.9 + - + +
790A ASN 5.0 0.9 - - - +
807A PHE* 3.7 23.5 - - + -
811A GLU* 4.1 1.4 + - - +
812A TYR* 1.3 74.1 - - - +
814A LEU* 1.3 65.2 + - - +
831A VAL* 3.7 14.4 - - + -
832A GLY 3.5 5.8 - - - -
833A THR* 3.8 4.7 - - - +
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Residues in contact with LEU 814 (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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722A ARG* 5.1 2.2 - - - +
723A LYS* 2.8 27.9 + - - +
736A LEU* 4.0 5.6 - - - -
812A TYR* 3.5 16.6 - - + +
813A ALA* 1.3 80.1 - - - +
815A SER* 1.3 56.8 + - - +
832A GLY 2.7 11.2 + - - +
833A THR 4.6 0.2 - - - +
834A ALA* 3.8 17.9 - - + -
869A ALA* 4.1 3.1 - - + -
870A VAL 3.5 26.0 - - - +
871A TYR* 3.6 13.3 - - + +
11B LEU* 3.8 26.2 - - + -
15B ARG* 2.7 35.9 - - - +
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Residues in contact with SER 815 (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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723A LYS* 4.2 4.9 - - - +
736A LEU* 3.7 2.2 - - - +
814A LEU* 1.3 78.2 - - - +
816A LEU* 1.3 63.1 + - - +
831A VAL* 3.2 10.7 - - - +
832A GLY* 3.0 30.6 + - - -
870A VAL* 2.6 27.4 + - - +
871A TYR 3.4 9.6 + - - -
872A SER* 3.8 9.0 - - - -
873A MET* 3.8 24.9 - - - -
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Residues in contact with LEU 816 (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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723A LYS* 4.2 14.4 - - + +
724A ILE* 3.9 7.9 - - - +
725A CYS* 2.9 37.0 - - + +
734A GLY* 3.4 33.0 - - - +
735A VAL 4.1 2.5 - - - +
736A LEU* 3.9 18.1 - - + +
791A LEU* 3.7 14.8 - - + -
815A SER* 1.3 75.8 - - - +
817A VAL* 1.3 70.3 + - - +
829A PHE* 4.9 5.6 - - + -
830A ILE 3.5 4.7 - - - +
831A VAL* 3.4 30.3 - - + -
873A MET* 5.0 1.2 + - - +
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Residues in contact with VAL 817 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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725A CYS* 3.9 5.4 - - - -
815A SER 4.3 0.2 - - - -
816A LEU* 1.3 79.2 - - - +
818A SER* 1.3 63.1 + - - +
819A CYS* 3.6 27.4 - - + -
829A PHE* 3.2 9.0 - - - -
830A ILE* 2.9 53.1 + - + +
873A MET* 2.8 38.8 - - + +
874A VAL* 4.3 1.3 - - - -
875A GLU* 4.2 13.9 - - + +
880A LEU* 4.9 5.2 - - + -
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Residues in contact with SER 818 (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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725A CYS* 4.1 9.1 - - - -
726A TYR 3.8 13.9 + - - +
727A GLN* 2.9 36.0 + - - +
817A VAL* 1.3 76.5 - - - +
819A CYS* 1.3 62.2 + - - +
827A THR* 3.9 2.4 - - - +
828A TYR 2.9 6.1 - - - -
829A PHE* 3.5 20.6 - - - -
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Residues in contact with CYS 819 (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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817A VAL* 3.6 24.2 - - - -
818A SER* 1.3 75.9 + - - +
820A LYS* 1.3 58.7 - - - +
821A LEU* 3.9 12.5 - - - +
827A THR* 3.8 7.4 - - - +
828A TYR* 2.6 41.6 + - - -
830A ILE* 3.6 17.7 - - - -
875A GLU* 3.5 40.4 - - + +
880A LEU* 5.8 0.9 - - - -
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Residues in contact with LYS 820 (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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729A VAL* 6.3 1.1 - - + -
819A CYS* 1.3 77.0 - - - +
821A LEU* 1.3 70.0 + - - +
822A GLY 4.4 2.4 + - - +
824A ASP 4.0 7.6 - - - +
825A PRO* 4.3 22.0 - - - +
826A ASN 2.9 23.8 - - - +
827A THR* 3.3 20.5 - - - +
875A GLU* 4.5 5.2 - - - +
878A GLY* 4.8 5.7 - - - -
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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