Contacts of the helix formed by residues 645 - 651 (chain B) in PDB entry 3ZHT
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 ASP 645 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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644B GLY* 1.3 72.2 - - - +
646B ALA* 1.4 64.7 + - - +
648B PHE* 3.8 0.4 + - - -
649B ALA* 3.5 12.5 + - - +
675B VAL* 3.7 11.3 - - - +
676B VAL 3.7 2.1 + - - +
677B ASN* 3.3 36.1 - - - +
678B ASN* 3.0 27.6 + - - +
679B GLN* 3.5 5.3 - - - -
680B ILE* 3.2 27.1 + - - +
686B PRO* 4.6 6.8 - - - +
690B ARG* 4.8 4.6 + - - +
695B CYS* 3.4 27.4 - - + +
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Residues in contact with ALA 646 (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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950A LEU* 3.6 28.5 + - + +
644B GLY 3.4 0.8 - - - -
645B ASP* 1.4 84.3 + - - +
647B ALA* 1.3 57.5 + - - +
649B ALA* 3.5 3.0 + - - +
650B GLY* 3.1 21.1 + - - -
680B ILE 4.8 0.4 + - - +
681B GLY* 3.9 27.8 - - - +
689B SER* 4.1 26.9 - - - +
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Residues in contact with ALA 647 (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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950A LEU* 3.6 19.0 - - + +
606B LEU* 3.9 25.4 - - + -
607B GLU* 3.3 25.3 - - + +
644B GLY* 3.6 10.9 + - - +
645B ASP 3.4 0.2 - - - -
646B ALA* 1.3 75.3 - - - +
648B PHE* 1.3 65.8 + - - +
651B GLN* 3.1 30.9 + - + +
654B VAL* 4.2 0.2 - - - +
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Residues in contact with PHE 648 (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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607B GLU* 3.3 5.1 + - - +
643B HIS* 3.3 47.1 - + + -
644B GLY 3.1 19.5 + - - +
645B ASP 4.2 4.0 - - - +
646B ALA 3.5 0.2 - - - -
647B ALA* 1.3 75.4 - - - +
649B ALA* 1.3 58.7 + - - +
651B GLN 4.5 1.0 - - - +
654B VAL* 3.5 43.5 - - + +
658B LEU* 4.8 6.3 - - + -
673B HIS* 4.3 9.4 - + - -
675B VAL* 3.9 16.4 - - + -
695B CYS 3.2 20.4 - - - +
696B THR* 3.6 29.4 - - + -
698B VAL* 3.7 18.8 - - + +
699B ALA* 4.9 0.9 - - + -
736B VAL* 4.5 15.5 - - + -
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Residues in contact with ALA 649 (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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655A ALA 5.6 0.3 - - - -
656A GLU* 5.5 0.7 - - - -
659A ASN* 3.4 19.2 - - - +
701A MET* 3.7 16.3 - - + +
645B ASP 3.5 12.1 + - - +
646B ALA* 3.5 4.6 + - - +
647B ALA 3.2 0.4 - - - -
648B PHE* 1.3 80.4 - - - +
650B GLY* 1.3 59.3 + - - +
651B GLN 5.1 1.2 - - - +
689B SER* 4.2 4.5 - - - +
690B ARG* 3.8 29.8 - - + -
692B SER* 5.7 0.4 - - - +
694B TYR 5.6 0.2 - - - +
695B CYS* 3.9 19.0 + - - +
698B VAL* 5.6 1.1 - - - -
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Residues in contact with GLY 650 (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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656A GLU* 3.3 18.2 - - - +
659A ASN* 4.1 9.6 - - - -
950A LEU 3.2 20.8 - - - +
951A SER* 2.7 24.7 + - - -
646B ALA 3.1 14.3 + - - -
647B ALA 3.3 0.2 + - - -
649B ALA* 1.3 78.8 - - - +
651B GLN* 1.3 59.4 + - - +
689B SER 4.9 0.4 - - - -
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Residues in contact with GLN 651 (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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655A ALA* 5.7 1.3 - - - +
656A GLU* 3.9 5.2 + - - +
950A LEU* 2.8 40.8 + - + +
951A SER* 3.9 4.0 - - - +
952A GLU* 3.2 26.6 + - - +
606B LEU 3.7 23.4 - - - +
607B GLU* 3.9 18.2 - - + -
647B ALA* 3.1 19.9 + - - +
648B PHE 4.5 1.2 - - - +
649B ALA 3.7 0.9 - - - +
650B GLY* 1.3 74.2 - - - +
652B GLY* 1.3 64.4 + - - +
653B VAL* 4.2 9.2 + - + +
654B VAL* 3.2 20.4 + - - +
655B ALA* 4.4 0.7 + - - +
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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