Contacts of the strand formed by residues 672 - 678 (chain B) in PDB entry 2H5G
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 GLU 672 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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605B LYS* 2.8 25.3 + - - -
642B VAL* 4.1 1.3 - - - -
643B LYS* 3.4 19.3 - - + +
645B HIS* 2.6 33.5 + - - +
668B TYR* 3.5 29.7 - - + -
670B ASP* 2.8 36.1 + - - +
671B LEU* 1.3 78.3 - - - +
673B LEU* 1.3 60.8 + - - +
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Residues in contact with LEU 673 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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601B VAL* 4.9 0.9 - - + -
605B LYS* 3.9 10.1 - - + -
615B LEU* 3.8 21.5 - - + -
616B GLU 3.5 24.9 - - - +
618B LEU* 3.8 20.6 - - + +
637B LEU* 3.9 31.4 - - + -
642B VAL* 3.7 12.3 - - + -
643B LYS 2.9 7.6 + - - +
644B ILE* 3.4 6.6 - - + +
645B HIS* 2.8 27.2 + - - -
668B TYR* 4.2 4.5 - - - -
672B GLU* 1.3 76.5 - - - +
674B CYS* 1.3 72.8 + - - +
675B ILE* 3.6 19.5 + - + -
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Residues in contact with CYS 674 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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616B GLU 3.1 9.3 + - - +
617B THR* 3.3 23.9 - - - +
618B LEU 2.7 31.7 + - - +
645B HIS* 3.1 14.1 - - + +
647B GLY 4.5 2.2 - - - -
661B VAL* 4.5 8.5 - - + -
664B LEU* 3.6 32.8 - - - -
668B TYR* 3.8 19.6 - - + +
673B LEU* 1.3 75.4 - - - +
675B ILE* 1.3 68.1 + - - +
676B GLU* 4.2 1.6 - - - -
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Residues in contact with ILE 675 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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618B LEU* 3.4 15.5 - - + +
620B ILE* 3.4 28.5 - - + -
630B PHE* 4.7 0.9 - - + -
633B ILE* 5.0 1.6 - - + -
634B ILE* 4.9 10.1 - - + -
637B LEU* 3.9 24.9 - - + -
644B ILE* 3.9 25.6 - - + -
645B HIS 2.9 5.9 + - - -
646B ALA* 3.5 1.0 - - - -
647B GLY 2.8 23.6 + - - -
650B PHE* 3.1 40.2 - - + -
673B LEU* 3.6 14.9 + - + -
674B CYS* 1.3 75.6 - - - +
676B GLU* 1.3 62.7 + - - +
677B VAL* 5.7 0.2 - - + -
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Residues in contact with GLU 676 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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618B LEU 2.8 8.0 + - - +
619B LEU* 3.2 25.5 - - + -
620B ILE* 2.8 25.0 + - - +
647B GLY* 3.4 11.8 - - - -
648B PRO* 3.3 13.0 - - - +
649B LYS* 3.0 28.5 + - - +
650B PHE* 2.5 32.3 + - - +
664B LEU* 4.7 5.0 - - + +
674B CYS* 4.0 10.0 - - - -
675B ILE* 1.3 78.0 - - - +
677B VAL* 1.3 77.6 + - - +
678B VAL* 4.8 0.7 - - + -
687B HIS* 4.3 15.7 - - + +
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Residues in contact with VAL 677 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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620B ILE* 3.1 13.9 - - + +
622B ARG* 4.0 19.7 - - + +
625B LEU* 3.5 27.4 - - + -
630B PHE* 6.0 0.4 - - + -
649B LYS* 3.5 34.4 - - + +
650B PHE* 3.6 31.4 - - + +
653B TYR* 4.0 8.1 - - + -
675B ILE* 5.7 0.7 - - + -
676B GLU* 1.3 90.7 + - - +
678B VAL* 1.3 81.0 + - - +
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Residues in contact with VAL 678 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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587B TYR* 3.6 35.7 - - + -
619B LEU* 4.0 25.6 - - + -
620B ILE 2.7 16.2 + - - +
621B HIS* 3.6 1.3 - - - -
622B ARG* 3.2 23.7 + - - +
649B LYS* 4.8 1.1 - - - +
676B GLU* 4.8 1.8 - - + -
677B VAL* 1.3 85.9 - - - +
679B ASP* 1.3 64.9 + - - +
680B ASN 4.0 8.7 - - - +
683B ASP* 3.6 20.6 - - + +
684B ALA* 4.2 13.0 - - + +
687B HIS* 4.8 5.4 - - + +
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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