Contacts of the helix formed by residues 629 - 639 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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672A GLN* 4.8 3.4 - - + +
625F MET 2.7 23.4 + - - +
626F CYS 3.9 1.3 - - - -
628F THR* 1.3 70.3 - - - +
630F GLY* 1.3 60.6 + - - +
631F GLY 3.3 2.6 + - - -
632F ARG* 3.7 11.2 + - + +
633F VAL* 3.3 27.2 + - + +
649F ASP 5.9 0.2 - - - -
650F LEU* 3.7 30.3 - - + -
653F VAL* 3.9 17.3 - - + -
705F ILE* 3.9 17.0 - - + +
708F ALA* 3.7 37.5 - - + +
709F TYR* 3.8 16.6 - - + +
712F THR* 4.1 10.1 - - - +
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Residues in contact with GLY 630 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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577F GLY* 3.7 18.0 - - - -
581F ALA* 4.2 2.7 - - - -
626F CYS 3.4 4.9 + - - -
627F MET 3.2 12.6 + - - -
628F THR 3.1 4.2 - - - -
629F LEU* 1.3 79.4 - - - +
631F GLY* 1.3 60.0 + - - +
634F SER* 3.3 23.4 + - - -
712F THR* 3.7 16.2 - - - -
716F LEU* 3.5 8.5 - - - +
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Residues in contact with GLY 631 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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574F HIS* 3.2 50.0 + - - -
578F HIS* 3.3 13.0 - - - -
629F LEU 3.3 0.6 - - - -
630F GLY* 1.3 76.5 - - - +
632F ARG* 1.3 64.4 + - - +
634F SER* 3.3 3.6 + - - -
635F GLU* 3.2 20.4 + - - +
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Residues in contact with ARG 632 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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664A PHE* 5.8 0.2 - - - +
665A GLY* 2.9 40.6 + - - +
666A MET* 3.8 2.8 - - - +
672A GLN* 3.0 24.8 + - - +
574F HIS* 3.8 6.5 + - - -
628F THR 5.2 1.0 + - - +
629F LEU* 3.7 13.3 + - + +
630F GLY 3.5 0.4 - - - -
631F GLY* 1.3 73.0 - - - +
633F VAL* 1.3 66.3 + - + +
635F GLU* 3.4 12.4 + - - +
636F GLU* 3.2 22.2 + - - +
642F ILE* 3.4 41.7 - - + +
643F THR 3.3 22.8 + - - +
646F ALA* 3.9 24.5 - - + +
649F ASP* 6.3 0.6 - - + +
650F LEU* 4.1 21.2 - - + +
709F TYR* 5.3 8.6 - - + -
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Residues in contact with VAL 633 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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629F LEU* 3.3 18.8 + - + +
630F GLY 4.1 1.6 - - - +
631F GLY 3.3 0.6 - - - -
632F ARG* 1.3 76.0 - - + +
634F SER* 1.3 57.9 + - - +
636F GLU* 3.2 7.3 + - + +
637F ILE* 3.0 44.4 + - + +
709F TYR* 3.6 33.0 - - + -
712F THR* 3.8 25.4 - - + +
713F VAL* 3.7 33.4 - - + -
716F LEU* 4.0 3.6 - - + -
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Residues in contact with SER 634 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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573F TYR* 2.6 29.4 + - - +
577F GLY* 3.8 10.8 - - - -
630F GLY 3.3 17.3 + - - -
631F GLY 3.6 3.1 - - - -
632F ARG 3.3 0.4 - - - -
633F VAL* 1.3 80.2 - - - +
635F GLU* 1.3 59.8 + - - +
637F ILE* 4.3 5.1 - - - +
638F PHE* 3.3 29.3 + - - +
716F LEU* 4.2 8.7 - - - +
723F VAL* 3.6 19.3 - - - +
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Residues in contact with GLU 635 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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615A LEU* 5.4 2.4 - - - +
570F THR* 3.7 21.6 - - + +
573F TYR* 4.9 0.7 - - - -
574F HIS* 3.3 40.5 + - + +
631F GLY 3.2 11.9 + - - +
632F ARG* 3.7 12.1 - - - +
633F VAL 3.2 0.2 - - - -
634F SER* 1.3 77.3 - - - +
636F GLU* 1.3 55.0 + - - +
639F PHE* 2.7 49.2 + - + +
641F ARG 3.9 11.1 + - - +
642F ILE* 4.5 1.7 - - - -
643F THR* 2.8 45.3 + - - +
645F GLY* 5.7 0.9 - - - -
646F ALA* 5.6 1.0 - - - +
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Residues in contact with GLU 636 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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632F ARG* 3.2 12.9 + - - +
633F VAL* 3.2 6.4 + - + +
635F GLU* 1.3 76.8 - - - +
637F ILE* 1.3 64.5 + - + +
640F GLY* 2.9 32.8 + - - +
641F ARG 4.4 2.6 + - - +
642F ILE* 4.2 23.0 - - + +
709F TYR* 2.3 33.3 + - - -
713F VAL* 5.7 0.6 - - - +
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Residues in contact with ILE 637 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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633F VAL* 3.0 31.8 + - + +
634F SER* 4.3 5.2 - - - +
636F GLU* 1.3 81.2 - - + +
638F PHE* 1.3 69.1 + - + +
639F PHE* 3.5 0.9 + - - -
640F GLY 4.6 0.5 + - - -
713F VAL* 4.6 6.5 - - + +
716F LEU* 3.8 30.5 - - + +
717F THR* 4.0 21.8 - - - +
720F LYS* 3.7 42.9 + - + +
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Residues in contact with PHE 638 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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573F TYR* 3.4 56.0 - + + -
634F SER* 3.3 17.9 + - - +
637F ILE* 1.3 88.1 - - + +
639F PHE* 1.3 71.1 + - + +
720F LYS* 3.6 49.1 - - + -
723F VAL* 3.6 25.6 - - + -
724F GLU* 3.9 24.2 - - + -
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Residues in contact with PHE 639 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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566F GLU* 5.2 8.1 - - - -
569F LYS* 3.8 31.9 - - + -
570F THR* 3.9 32.5 - - + -
573F TYR* 3.4 38.8 - + + -
635F GLU* 2.7 35.9 + - + +
637F ILE 3.3 1.1 - - - -
638F PHE* 1.3 83.6 - - + +
640F GLY* 1.3 60.4 + - - +
641F ARG* 3.6 37.6 + - + +
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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