Contacts of the strand formed by residues 725 - 730 (chain A) in PDB entry 6F3T
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 ILE 725 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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453A LEU* 3.8 25.1 - - + -
454A GLY* 3.8 15.7 - - - +
458A LEU* 4.1 3.1 - - + -
459A PRO* 4.0 18.4 - - + -
718A ARG 4.1 0.2 - - - +
719A PHE* 3.3 4.9 - - - -
720A SER* 2.7 40.8 + - - +
723A GLY 3.3 0.4 - - - -
724A GLU* 1.3 83.5 - - - +
726A LEU* 1.3 71.9 + - - +
727A ALA 4.4 0.4 - - - +
737A LEU* 4.2 19.7 - - + -
738A TRP 3.3 14.1 - - - +
739A ASP* 5.0 0.4 - - - +
740A ALA* 4.1 4.5 - - - -
770A LEU* 3.8 22.7 - - + -
785A PHE* 4.6 10.5 - - + -
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Residues in contact with LEU 726 (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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676A THR* 4.2 6.3 - - + -
685A ALA* 4.0 4.3 - - + -
693A VAL* 3.9 27.6 - - + -
695A LEU* 3.9 19.3 - - + -
707A LEU* 3.9 12.3 - - + -
717A LEU* 4.3 5.6 - - + -
718A ARG 3.6 26.2 - - - +
719A PHE* 3.8 31.9 - - + -
725A ILE* 1.3 75.8 - - - +
727A ALA* 1.3 66.7 + - - +
737A LEU* 3.4 1.9 - - - -
738A TRP* 2.8 52.3 + - + +
740A ALA* 4.1 4.8 - - + +
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Residues in contact with ALA 727 (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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717A LEU* 3.3 7.8 - - - +
718A ARG 2.7 40.7 + - - +
725A ILE 4.2 0.6 - - - -
726A LEU* 1.3 74.6 - - - +
728A SER* 1.3 60.7 + - - +
735A VAL* 4.9 1.8 - - + -
736A ARG 3.4 4.7 - - - -
737A LEU* 3.7 20.4 - - + -
783A LEU* 3.6 21.9 - - + +
785A PHE* 4.1 16.8 - - + -
791A VAL* 5.6 2.2 - - + -
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Residues in contact with SER 728 (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 VAL* 4.2 3.4 - - - -
710A HIS* 2.8 31.8 + - - -
714A VAL* 4.2 4.3 - - - -
716A SER 3.4 5.6 - - - -
717A LEU* 3.6 19.1 - - - -
727A ALA* 1.3 75.9 - - - +
729A GLY* 1.3 58.2 + - - +
735A VAL* 3.2 6.6 - - - +
736A ARG* 2.9 31.6 + - - +
738A TRP* 3.0 25.6 + - - -
783A LEU* 3.8 4.7 - - - -
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Residues in contact with GLY 729 (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 HIS* 4.5 0.2 - - - -
714A VAL* 3.5 6.5 - - - +
715A CYS 2.9 21.8 + - - -
716A SER* 3.0 29.0 + - - -
728A SER* 1.3 73.7 - - - +
730A SER* 1.3 60.6 + - - -
734A THR 3.8 4.9 - - - -
735A VAL* 4.2 11.2 - - - -
780A VAL* 3.9 9.4 - - - -
783A LEU* 3.6 1.4 - - - +
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Residues in contact with SER 730 (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 HIS* 3.1 24.5 - - - -
712A ASP 3.1 12.9 + - - -
713A THR 2.8 15.6 + - - -
714A VAL* 4.4 0.2 - - - -
715A CYS* 3.9 7.8 - - - -
729A GLY* 1.3 74.4 - - - -
731A MET* 1.3 60.9 + - - +
732A ASP* 3.0 31.2 + - - -
733A ASN* 3.0 20.1 + - - -
734A THR 3.3 5.9 + - - +
779A PRO* 3.8 10.4 - - - +
780A VAL 4.1 3.2 + - - +
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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