Contacts of the strand formed by residues 651 - 660 (chain G) in PDB entry 3HR4
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 SER 651 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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618G LYS* 3.5 14.8 + - - +
619G PHE 3.0 8.3 + - - -
620G ARG* 2.8 53.1 + - - +
621G TYR* 3.0 1.9 + - - -
649G GLY 4.1 5.4 + - - -
650G ALA* 1.3 68.4 - - - +
652G GLN* 1.3 61.6 + - - +
653G LEU 2.8 7.6 + - - -
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Residues in contact with GLN 652 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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620G ARG* 5.5 0.4 - - - -
621G TYR* 2.9 43.3 + - + +
642G ASP* 2.9 30.6 + - - +
646G SER* 5.4 0.7 - - - -
650G ALA 3.4 1.8 + - - -
651G SER* 1.3 66.9 - - - +
653G LEU* 1.3 64.0 + - - +
654G THR* 3.0 20.5 + - - +
655G PRO* 3.0 30.9 - - - +
656G MET 3.5 2.4 - - - +
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Residues in contact with LEU 653 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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585G LEU* 4.6 11.0 - - + -
620G ARG* 4.3 19.7 - - + +
621G TYR 2.6 24.0 + - - +
622G ALA* 4.5 2.9 - - + -
651G SER 2.8 6.0 + - - -
652G GLN* 1.3 72.1 - - - +
654G THR* 1.3 58.5 + - - +
675G GLN* 5.4 0.2 - - - +
676G THR* 3.3 37.2 - - - +
679G ALA* 3.0 43.8 - - + +
680G ALA* 4.0 7.9 - - + -
683G THR* 3.7 20.4 - - + +
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Residues in contact with THR 654 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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621G TYR 4.0 0.8 + - - -
622G ALA* 4.1 10.7 - - + -
623G VAL 4.8 0.2 + - - -
652G GLN* 3.0 21.1 - - - +
653G LEU* 1.3 86.8 - - - +
655G PRO* 1.4 82.6 + - - +
656G MET* 3.4 1.2 + - - -
672G TRP* 3.2 25.0 - - + +
675G GLN* 3.3 28.7 + - - +
676G THR* 3.2 31.9 - - - +
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Residues in contact with PRO 655 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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652G GLN* 3.0 14.8 - - - +
654G THR* 1.4 94.4 + - - +
656G MET* 1.3 69.5 + - - +
657G GLY* 3.0 4.5 + - - -
672G TRP* 3.6 11.6 + - - -
675G GLN* 5.1 2.2 - - - +
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Residues in contact with MET 656 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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623G VAL* 2.9 29.2 - - + +
625G GLY 4.1 1.1 - - - +
635G CYS* 3.9 13.7 - - + -
638G ALA* 3.8 20.4 - - + -
639G HIS* 3.7 51.6 + - + +
642G ASP* 2.9 43.7 + - - +
652G GLN* 3.5 6.3 - - - +
654G THR 3.4 3.7 + - - -
655G PRO* 1.3 72.0 - - - +
657G GLY* 1.3 75.2 + - - +
658G GLU* 3.9 12.7 + - + +
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Residues in contact with GLY 657 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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623G VAL 3.1 8.3 + - - -
624G PHE* 3.4 19.1 - - - -
625G GLY 3.0 25.1 + - - -
655G PRO 3.0 5.3 + - - -
656G MET* 1.3 78.7 - - - +
658G GLU* 1.3 61.6 + - - -
672G TRP* 3.6 13.1 - - - -
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Residues in contact with GLU 658 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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624G PHE* 3.9 2.6 - - - -
625G GLY 3.7 2.5 - - - -
634G PHE* 3.0 60.6 - - + +
635G CYS* 3.7 4.6 - - - +
639G HIS* 4.1 12.8 + - - +
656G MET* 3.9 18.1 + - + +
657G GLY* 1.3 75.4 - - - -
659G GLY* 1.3 53.2 + - - +
660G ASP* 2.8 18.4 + - + +
668G ALA* 3.4 14.9 - - - +
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Residues in contact with GLY 659 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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624G PHE* 3.3 27.0 - - - -
625G GLY 2.5 22.6 + - - -
626G LEU* 4.4 0.4 - - - -
627G GLY 3.7 8.4 + - - -
634G PHE* 4.5 0.9 - - - -
635G CYS* 4.4 0.2 - - - -
658G GLU* 1.3 66.5 - - - +
660G ASP* 1.3 64.8 + - - -
661G GLU 2.9 4.7 + - - -
665G GLN* 3.1 28.3 + - - +
668G ALA* 4.1 4.0 - - - -
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Residues in contact with ASP 660 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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629G SER* 3.2 26.0 + - - -
634G PHE* 3.5 32.8 - - + -
658G GLU* 2.8 13.9 + - + +
659G GLY* 1.3 68.4 - - - +
661G GLU* 1.3 66.3 + - - +
662G LEU* 3.1 21.2 + - - +
663G SER* 3.1 28.1 + - - -
664G GLY 3.1 8.8 + - - -
665G GLN 3.1 17.2 + - - -
668G ALA* 4.3 3.8 - - + +
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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