Contacts of the strand formed by residues 647 - 650 (chain A) in PDB entry 3SHW
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 647 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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645A ARG 4.2 2.5 - - - +
646A PRO* 1.3 77.2 - - - +
648A THR* 1.3 66.2 + - - +
649A ILE* 3.8 22.2 - - + +
669A TYR* 4.8 0.7 - - + -
703A HIS* 3.8 22.7 - - + +
704A ALA 2.7 11.5 + - - +
705A LEU* 3.4 16.8 - - + +
706A LEU 2.8 26.0 + - - -
724A ILE* 3.4 14.8 - - + +
726A VAL* 4.6 3.8 - - + -
790A ILE* 3.8 46.4 - - + -
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Residues in contact with THR 648 (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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647A VAL* 1.3 74.1 - - - +
649A ILE* 1.3 65.7 + - - +
650A PHE* 4.2 5.7 - - - -
706A LEU* 3.5 43.1 - - + -
708A VAL* 3.7 16.6 - - + -
713A VAL* 4.0 12.8 - - + +
716A LEU* 5.2 0.4 - - + -
723A PRO* 4.5 9.2 - - + -
724A ILE 3.0 4.9 + - - +
725A VAL* 3.4 29.2 - - - +
726A VAL 3.0 23.9 + - - +
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Residues in contact with ILE 649 (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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647A VAL* 3.8 18.4 - - + +
648A THR* 1.3 80.7 - - - +
650A PHE* 1.3 70.3 + - - +
654A ALA* 3.2 23.3 - - + +
657A ALA* 4.0 14.1 - - + -
658A ARG* 3.6 27.9 + - + +
661A LEU* 3.8 29.2 - - + -
705A LEU* 4.8 1.8 - - + -
706A LEU 4.3 5.0 + - - +
726A VAL* 3.3 17.9 - - + +
728A LEU* 3.8 32.1 - - + -
786A LEU* 4.0 9.6 - - + -
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Residues in contact with PHE 650 (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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648A THR* 4.2 7.4 - - - -
649A ILE* 1.3 79.3 - - - +
651A GLY* 1.3 60.7 + - - +
654A ALA* 4.0 3.6 - - - -
708A VAL* 3.8 16.2 - - + -
709A THR 4.3 0.4 - - - -
710A PRO* 3.8 33.2 - - + -
713A VAL* 3.8 26.0 - - + -
725A VAL* 3.5 32.3 - - + -
726A VAL 2.9 8.5 + - - +
727A PHE* 3.9 9.9 - - + -
728A LEU* 2.9 28.4 + - - +
757A ARG* 4.4 6.5 - - - -
761A LEU* 3.5 35.0 - - + -
768A LEU* 5.7 4.3 - - + -
769A PHE* 4.1 14.1 - + - -
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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