Contacts of the strand formed by residues 755 - 761 (chain A) in PDB entry 3KSS
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 MET 755 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54A PRO* 5.4 12.3 - - + +
186A GLU* 5.3 3.1 - - - +
270A GLU* 5.2 5.2 - - - +
753A GLY 3.0 8.0 + - - +
754A ALA* 1.3 70.8 - - - +
756A VAL* 1.3 60.3 + - - +
757A GLY* 3.5 21.5 + - - +
758A GLU* 3.3 45.5 - - + +
765A ARG* 4.1 13.0 - - - +
767A PRO* 3.7 13.5 - - + -
768A ILE 3.3 11.0 - - - +
769A ASN* 4.5 2.0 - - - +
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Residues in contact with VAL 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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207A LYS* 4.2 25.1 - - + +
210A LEU* 3.4 33.4 - - + +
211A ASP* 3.4 30.5 + - - +
754A ALA 3.2 6.2 + - - +
755A MET* 1.3 71.3 - - - +
757A GLY* 1.3 56.3 + - - +
768A ILE* 2.8 27.3 + - + +
770A LEU* 4.0 17.3 - - + -
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Residues in contact with GLY 757 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
755A MET* 3.3 12.7 + - - +
756A VAL* 1.3 80.7 - - - +
758A GLU* 1.3 58.3 + - - +
765A ARG* 5.1 2.7 - - - -
768A ILE* 2.5 45.0 + - - +
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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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214A ASN* 3.5 15.0 + - - -
270A GLU* 5.3 0.7 - - - +
755A MET* 3.3 31.0 - - + +
757A GLY* 1.3 72.5 - - - -
759A THR* 1.3 61.6 + - - +
760A VAL* 4.1 2.6 + - - +
765A ARG* 2.5 77.9 + - + +
766A TYR 3.0 10.3 - - - +
767A PRO* 3.3 29.3 - - + +
768A ILE 4.2 0.4 - - - +
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Residues in contact with THR 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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187A TYR* 3.0 37.3 - - + -
214A ASN* 4.1 9.0 - - - +
237A LEU* 4.3 15.7 - - + +
243A PHE* 3.9 8.3 - - + -
758A GLU* 1.3 72.5 - - - +
760A VAL* 1.3 62.1 + - - +
761A GLU* 3.2 10.4 + - - +
765A ARG* 3.3 19.7 - - - -
766A TYR 2.8 15.0 + - - +
768A ILE* 3.3 37.0 - - + -
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Residues in contact with VAL 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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214A ASN* 5.0 3.1 - - - +
236A TYR* 3.2 48.3 - - + +
237A LEU 4.9 5.9 + - - +
238A GLN* 5.5 6.2 + - - +
758A GLU 5.1 3.1 - - - +
759A THR* 1.3 72.4 - - - +
761A GLU* 1.3 63.5 + - - +
762A GLY* 4.2 1.5 + - - -
763A ILE 5.5 3.1 - - - +
764A ALA 3.4 12.3 - - - +
765A ARG* 4.8 8.7 - - + +
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Residues in contact with GLU 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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185A LYS* 4.1 9.0 + - - -
187A TYR* 2.5 32.1 + - - -
237A LEU 5.7 0.2 - - - +
238A GLN* 6.1 1.3 - - - -
759A THR* 3.2 22.4 + - - +
760A VAL* 1.3 78.2 - - - +
762A GLY* 1.3 70.7 + - - +
763A ILE 2.9 0.7 + - - -
764A ALA* 2.3 31.2 + - + +
766A TYR* 3.8 22.8 - - + -
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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