Contacts of the helix formed by residues 629 - 639 (chain B) in PDB entry 6NYY
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 LEU 629 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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625B MET 3.1 21.0 + - - +
626B CYS 4.3 4.3 - - - +
628B THR* 1.3 74.5 - - - +
630B GLY* 1.3 63.3 + - - +
631B GLY 3.3 1.1 - - - -
632B ARG* 3.3 11.6 + - - +
633B VAL* 3.2 28.9 + - + +
649B ASP* 5.6 0.2 - - - -
650B LEU* 3.8 24.0 - - + -
653B VAL* 3.7 29.4 - - + -
705B ILE* 4.0 6.3 - - + +
708B ALA* 3.7 13.9 - - + -
709B TYR* 3.7 40.4 - - + +
712B THR* 4.6 3.6 - - - +
672C GLN* 4.5 10.5 - - + -
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Residues in contact with GLY 630 (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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577B GLY* 3.4 19.3 - - - +
581B ALA* 4.5 0.7 - - - -
626B CYS 3.6 2.8 + - - -
627B MET 2.9 17.0 + - - -
629B LEU* 1.3 78.7 - - - +
631B GLY* 1.3 61.2 + - - +
633B VAL 3.4 0.2 + - - -
634B SER 3.2 17.8 + - - -
712B THR* 3.7 20.2 - - - -
716B LEU* 3.4 10.7 - - - +
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Residues in contact with GLY 631 (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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574B HIS* 3.1 40.7 + - - +
577B GLY* 3.9 0.4 - - - -
578B HIS* 3.4 29.0 + - - -
629B LEU 3.3 0.4 - - - -
630B GLY* 1.3 76.7 - - - +
632B ARG* 1.3 61.4 + - - +
634B SER* 3.4 3.1 + - - -
635B GLU* 3.2 18.0 + - - +
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Residues in contact with ARG 632 (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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574B HIS* 3.7 7.0 - - - -
578B HIS* 4.9 0.2 + - - -
628B THR 5.0 0.8 + - - +
629B LEU* 3.3 15.8 + - + +
631B GLY* 1.3 73.9 - - - +
633B VAL* 1.3 66.3 + - + +
635B GLU* 3.5 13.3 + - - +
636B GLU* 3.3 20.5 + - - +
642B ILE* 3.3 41.2 - - + +
643B THR 3.9 12.1 + - - -
645B GLY 3.9 2.8 + - - -
646B ALA* 3.8 21.2 + - + +
649B ASP* 6.0 0.2 - - + -
650B LEU* 3.4 36.7 - - + +
709B TYR* 5.4 5.8 - - + -
665C GLY* 2.8 41.4 + - - +
666C MET* 4.9 0.8 - - - +
672C GLN* 2.6 24.5 + - - +
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Residues in contact with VAL 633 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
629B LEU 3.2 15.3 + - - +
630B GLY 3.8 7.4 - - - +
631B GLY 3.3 0.2 - - - -
632B ARG* 1.3 78.8 - - - +
634B SER* 1.3 55.8 + - - +
636B GLU* 2.9 23.8 + - + +
637B ILE* 3.0 32.5 + - + +
709B TYR* 3.6 30.3 - - + -
712B THR* 3.8 22.0 - - + +
713B VAL* 3.7 32.5 - - + +
716B LEU* 4.2 5.2 - - + -
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Residues in contact with SER 634 (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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573B TYR* 2.7 26.6 + - - +
577B GLY* 3.7 13.7 - - - -
630B GLY 3.2 16.8 + - - -
631B GLY 3.9 2.2 - - - -
632B ARG 3.3 0.2 - - - -
633B VAL* 1.3 79.1 - - - +
635B GLU* 1.3 60.9 + - - +
637B ILE* 4.5 7.9 - - - +
638B PHE* 3.3 45.5 + - - +
716B LEU* 4.5 5.4 - - - +
723B VAL* 3.5 7.9 - - - +
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Residues in contact with GLU 635 (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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570B THR* 4.2 14.2 - - + +
573B TYR* 5.0 1.6 - - - -
574B HIS* 2.7 46.9 + - + +
631B GLY 3.2 11.8 + - - +
632B ARG* 3.7 14.6 - - - +
633B VAL 3.2 0.4 - - - -
634B SER* 1.3 77.6 - - - +
636B GLU* 1.3 58.5 + - - +
639B PHE* 3.2 40.0 + - + +
641B ARG 3.4 12.1 - - - +
642B ILE* 4.9 1.8 - - + +
643B THR* 2.8 42.0 + - + +
645B GLY* 4.5 6.5 - - - +
615C LEU* 5.5 1.6 - - - +
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Residues in contact with GLU 636 (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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632B ARG* 3.3 9.6 + - - +
633B VAL* 2.9 11.0 + - + +
635B GLU* 1.3 79.7 - - - +
637B ILE* 1.3 62.6 + - + +
640B GLY* 3.1 29.9 + - - +
641B ARG 4.5 0.7 - - - -
642B ILE* 4.0 24.6 - - + +
709B TYR* 2.3 32.2 + - - -
713B VAL* 5.5 1.3 - - - +
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Residues in contact with ILE 637 (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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633B VAL* 3.0 35.5 + - + +
634B SER* 4.4 4.9 - - - +
636B GLU* 1.3 81.9 - - + +
638B PHE* 1.3 66.9 + - + +
639B PHE 4.9 0.2 - - - -
640B GLY 4.8 0.7 + - - -
713B VAL* 4.7 4.5 - - + +
716B LEU* 3.4 26.9 - - + +
717B THR* 3.5 23.6 - - + +
720B LYS* 3.8 40.8 + - + +
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Residues in contact with PHE 638 (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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573B TYR* 3.5 49.7 - + + -
634B SER* 3.3 34.2 + - - +
637B ILE* 1.3 84.7 - - + +
639B PHE* 1.3 68.1 + - + +
716B LEU 6.0 0.4 - - - -
720B LYS* 3.8 41.7 - - + +
723B VAL* 3.6 32.8 - - + -
724B GLU* 3.9 22.4 - - + -
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Residues in contact with PHE 639 (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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566B GLU* 4.5 4.3 - - - -
569B LYS* 3.7 30.1 - - + -
570B THR* 3.5 38.4 - - + -
573B TYR* 3.4 40.8 - + + -
635B GLU* 3.2 23.3 + - + +
637B ILE 4.9 0.7 - - - -
638B PHE* 1.3 85.9 - - + +
640B GLY* 1.3 60.7 + - - +
641B ARG* 3.3 42.9 + - + +
643B THR* 5.9 2.2 - - + -
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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