Contacts of the strand formed by residues 753 - 762 (chain A) in PDB entry 3OSE
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 753 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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743A VAL* 3.3 5.9 - - - +
744A HIS* 2.9 35.5 + - + +
751A SER 3.6 6.3 - - - +
752A LEU* 1.3 78.0 - - - +
754A GLN* 1.3 66.5 + - - +
755A TRP* 3.7 18.9 - - + -
776A SER 3.6 12.1 - - - +
777A GLY* 4.6 3.6 - - - -
781A ALA* 3.3 42.2 - - + +
782A PHE* 3.8 28.0 - - + +
785A ILE* 4.1 11.4 - - + -
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Residues in contact with GLN 754 (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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741A PHE* 3.5 37.3 - - + -
742A CYS 3.2 7.6 - - - +
743A VAL* 4.2 15.9 - - + +
752A LEU* 4.7 15.9 - - + +
753A VAL* 1.3 80.0 - - - +
755A TRP* 1.3 64.4 + - - +
774A ARG* 4.1 0.9 - - - -
775A ILE* 2.9 27.0 + - + +
776A SER* 2.6 44.9 + - - +
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Residues in contact with TRP 755 (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 LEU* 3.9 16.2 - - + -
730A CYS* 3.7 25.6 - - + -
741A PHE* 3.7 2.2 - - - -
742A CYS* 2.7 56.3 + - + +
743A VAL 4.0 2.5 - - - -
744A HIS* 3.8 15.7 - - + -
753A VAL* 3.7 25.1 - - + -
754A GLN* 1.3 82.1 - - - +
756A GLU* 1.3 79.5 + - - +
757A MET* 3.3 23.5 - - + +
772A PHE* 3.9 19.2 - + + -
773A LYS 3.2 13.2 - - - +
775A ILE* 3.9 6.7 - - - +
782A PHE* 3.6 23.8 - + + -
785A ILE* 3.9 20.6 - - + -
786A ALA* 4.9 3.8 - - - +
789A ILE* 4.3 10.5 - - + -
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Residues in contact with GLU 756 (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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739A LEU* 4.4 12.3 - - + +
740A LEU 3.4 9.4 - - - +
741A PHE* 4.8 8.5 - - + +
755A TRP* 1.3 78.5 - - - +
757A MET* 1.3 60.5 + - - +
771A ARG* 2.8 39.4 + - - +
772A PHE* 3.3 6.1 - - - -
773A LYS* 2.8 43.6 + - + +
775A ILE* 3.7 30.5 - - + +
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Residues in contact with MET 757 (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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718A MET* 5.8 1.0 - - - +
721A ILE* 3.7 30.1 - - + -
725A LEU* 4.1 15.3 - - - -
738A PHE 4.0 0.3 - - - +
739A LEU* 3.5 3.3 - - - +
740A LEU* 2.9 38.9 + - + +
742A CYS* 3.9 18.6 - - - -
755A TRP* 3.3 32.5 + - + +
756A GLU* 1.3 74.8 - - - +
758A GLU* 1.3 59.9 + - - +
770A VAL* 3.8 15.3 - - + -
771A ARG 3.2 5.8 - - - +
772A PHE* 3.5 31.6 - - + -
789A ILE* 4.0 10.5 - - + -
793A LEU* 4.4 2.5 - - + -
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Residues in contact with GLU 758 (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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698A ARG* 2.8 58.3 + - - +
700A LEU* 4.5 6.5 - - - -
721A ILE* 5.8 0.2 - - - -
736A GLU* 5.0 5.4 - - - +
738A PHE* 3.2 15.8 - - - +
739A LEU* 3.8 17.7 - - + -
757A MET* 1.3 76.3 - - - +
759A VAL* 1.3 71.9 + - - +
760A CYS* 3.8 1.1 + - + -
769A GLY 3.7 0.3 - - - +
770A VAL* 3.4 4.8 - - - +
771A ARG* 2.8 66.2 + - + +
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Residues in contact with VAL 759 (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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697A PRO* 3.5 15.8 - - + +
714A PRO* 3.8 32.1 - - + +
717A MET* 3.9 33.7 - - + -
718A MET* 3.5 29.3 - - - -
721A ILE* 3.5 23.6 - - + -
738A PHE* 3.0 23.2 + - + +
758A GLU* 1.3 80.2 - - - +
760A CYS* 1.3 63.7 + - - +
768A ASN* 5.0 0.2 - - + -
769A GLY 3.4 3.4 - - - -
770A VAL* 4.3 1.8 - - + -
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Residues in contact with CYS 760 (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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697A PRO* 3.9 5.2 - - - -
698A ARG* 3.3 14.8 - - + +
700A LEU* 3.4 30.7 - - + -
706A MET* 3.9 23.3 - - - -
758A GLU* 4.7 7.2 - - + +
759A VAL* 1.3 76.2 - - - +
761A LYS* 1.3 61.8 + - - +
762A LEU* 4.1 13.7 - - - -
768A ASN* 3.2 7.0 - - - +
769A GLY* 2.8 45.8 + - - -
771A ARG* 4.9 0.9 - - - -
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Residues in contact with LYS 761 (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 LYS* 6.2 0.2 - - + -
697A PRO* 3.8 38.8 - - + +
698A ARG 2.8 6.5 + - - -
699A SER* 3.8 17.3 - - - +
700A LEU* 2.9 27.7 + - - +
714A PRO* 4.1 11.3 - - - +
760A CYS* 1.3 74.7 - - - +
762A LEU* 1.3 62.9 + - - +
763A PRO* 3.4 7.1 - - + +
767A LEU 4.7 0.7 - - - +
768A ASN* 3.0 36.3 + - - +
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Residues in contact with LEU 762 (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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700A LEU* 3.4 23.1 - - + +
701A ARG 4.5 1.3 - - - +
702A PHE* 4.3 18.8 - - + +
706A MET* 3.6 30.3 - - + -
709A THR* 3.7 19.5 - - + -
760A CYS* 4.1 13.0 - - - -
761A LYS* 1.3 77.1 - - - +
763A PRO* 1.3 66.4 - - - +
764A ARG 3.2 2.7 - - - -
765A LEU* 2.9 29.9 + - + -
766A SER 3.1 8.5 + - - -
767A LEU* 2.7 20.2 + - + +
768A ASN 3.9 3.8 - - - +
769A GLY* 3.8 17.7 - - - +
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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