Contacts of the strand formed by residues 671 - 677 (chain A) in PDB entry 4WGK
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 671 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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663A LYS* 5.9 0.7 - - - -
666A TYR* 3.5 13.0 + - - -
669A GLY 4.8 3.8 - - - +
670A GLU* 1.3 81.2 - - - +
672A ALA* 1.3 70.0 + - - +
673A GLU* 3.7 7.0 + - + +
734A GLU* 4.1 16.4 - - + +
735A TRP 3.4 7.6 - - - +
736A HIS* 3.3 48.0 - - + +
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Residues in contact with ALA 672 (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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662A ALA* 4.6 1.1 - - + -
666A TYR* 3.6 32.2 - - + +
670A GLU 4.1 1.0 - - - -
671A VAL* 1.3 72.4 - - - +
673A GLU* 1.3 59.1 + - - +
733A VAL 3.7 1.2 - - - +
734A GLU* 3.3 3.1 - - - -
735A TRP* 2.7 49.5 + - + +
737A ILE* 4.3 6.4 - - + +
748A ILE* 4.4 5.3 - - + +
775A PHE* 4.0 23.3 - - + -
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Residues in contact with GLU 673 (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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660A GLN* 3.8 22.2 - - - +
661A PRO 3.8 5.7 - - - +
662A ALA* 3.7 13.9 - - - +
666A TYR* 3.8 6.1 + - - -
671A VAL* 3.7 8.9 + - + +
672A ALA* 1.3 74.9 - - - +
674A VAL* 1.3 68.4 + - - +
675A ILE* 3.9 15.6 - - + +
732A THR* 3.7 24.9 - - + +
733A VAL 3.5 2.9 - - - -
734A GLU* 3.4 24.4 - - + +
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Residues in contact with VAL 674 (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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658A VAL* 4.2 9.0 - - + -
660A GLN 3.3 10.1 - - - +
661A PRO* 4.5 0.7 - - + -
662A ALA* 3.8 22.0 - - + +
673A GLU* 1.3 80.9 - - - +
675A ILE* 1.3 66.0 + - - +
676A PHE* 3.5 35.0 - - + -
731A ALA 3.8 1.4 - - - +
732A THR* 3.5 2.1 - - - +
733A VAL 3.0 34.6 + - - +
748A ILE* 3.7 25.8 - - + -
772A SER* 3.7 22.2 - - - +
775A PHE* 4.9 0.2 - - + -
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Residues in contact with ILE 675 (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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658A VAL* 3.6 5.7 - - - +
659A LEU* 2.8 38.3 + - + -
660A GLN* 2.9 51.9 + - + +
673A GLU* 3.9 14.6 - - + +
674A VAL* 1.3 77.2 - - - +
676A PHE* 1.3 65.3 + - - +
730A ASN* 3.7 33.4 - - + +
731A ALA 3.7 2.0 - - - +
732A THR* 3.8 22.0 - - + +
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Residues in contact with PHE 676 (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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656A GLY 3.3 20.6 - - - +
657A ASP 3.4 5.4 - - - +
658A VAL* 3.8 24.0 - - + -
659A LEU* 4.0 4.4 - - - +
674A VAL* 3.5 30.3 - - + -
675A ILE* 1.3 75.9 - - - +
677A VAL* 1.3 62.5 + - - +
730A ASN* 3.4 8.7 - - - +
731A ALA 2.9 42.3 + - - +
733A VAL* 4.0 14.1 - - + -
748A ILE* 3.6 21.1 - - + -
750A TYR* 3.6 44.9 - + + -
770A GLY* 3.9 19.1 - - - -
771A THR 4.0 1.1 - - - -
772A SER 4.1 1.6 - - - -
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Residues in contact with VAL 677 (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 ARG 4.5 1.6 - - - +
649A ALA* 4.0 6.1 - - + -
650A PRO* 3.6 29.6 - - + -
653A ARG* 5.0 1.3 - - + -
654A THR 3.1 22.7 - - - +
655A PHE* 3.9 25.0 - - + -
656A GLY* 3.1 22.5 + - - -
657A ASP* 3.0 23.9 + - + +
659A LEU* 3.6 24.8 - - + +
676A PHE* 1.3 72.8 - - - +
678A GLY* 1.3 61.5 + - - +
728A LEU* 5.6 0.2 - - + -
729A SER 3.7 6.7 - - - +
730A ASN* 4.8 0.2 - - - -
750A TYR* 3.9 2.8 - - - -
768A PHE* 4.4 0.2 - - - -
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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