Contacts of the helix formed by residues 646 - 659 (chain C) 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 ALA 646 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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574C HIS* 4.0 20.6 - - + -
632C ARG* 4.0 31.0 - - + -
635C GLU* 5.2 2.5 - - - +
643C THR* 4.2 8.6 + - - +
644C THR 3.3 1.8 - - - -
645C GLY* 1.3 75.0 - - - +
647C GLN* 1.3 62.9 + - - +
648C ASP 3.4 2.2 - - - -
649C ASP* 3.4 17.2 + - + +
650C LEU* 3.2 28.2 + - + +
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Residues in contact with GLN 647 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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644C THR 3.7 13.9 + - - +
645C GLY 3.2 3.8 + - - -
646C ALA* 1.3 77.9 - - - +
648C ASP* 1.3 67.4 + - - +
650C LEU* 3.3 9.4 + - - +
651C ARG* 3.2 34.8 + - - +
663D GLN* 3.1 50.8 - - - +
664D PHE* 3.3 26.8 - - + +
674D SER* 4.2 4.5 + - - +
7I ALA* 5.0 7.9 - - + +
8I ALA 5.1 3.6 - - - +
9I ALA 4.9 5.9 - - - +
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Residues in contact with ASP 648 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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601C LYS 5.4 1.2 - - - +
645C GLY 4.7 0.6 + - - -
646C ALA* 3.4 0.4 - - - +
647C GLN* 1.3 80.1 - - - +
649C ASP* 1.3 66.2 + - - +
651C ARG* 4.0 17.2 + - - +
652C LYS* 3.4 33.9 + - - +
5I ALA* 5.4 12.3 - - + +
7I ALA* 3.4 27.6 - - + +
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Residues in contact with ASP 649 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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574C HIS* 3.0 14.2 + - - -
578C HIS* 3.0 18.6 + - - -
628C THR* 3.4 28.2 - - - +
629C LEU* 5.4 1.8 - - + -
631C GLY* 4.9 0.2 - - - -
632C ARG* 5.1 1.5 + - + +
646C ALA* 3.4 15.6 + - + +
647C GLN 3.2 0.8 - - - -
648C ASP* 1.3 80.3 - - - +
650C LEU* 1.3 62.6 + - + +
652C LYS* 3.5 2.8 + - - +
653C VAL* 3.2 27.8 + - - +
802C ZN 2.1 36.8 - - - -
4I ALA* 4.2 6.1 - - - +
5I ALA 3.4 7.2 + - - +
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Residues in contact with LEU 650 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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629C LEU* 3.8 21.3 - - + -
632C ARG* 3.4 29.6 - - - +
646C ALA* 3.2 23.6 + - + +
647C GLN* 3.3 3.5 + - - +
649C ASP* 1.3 77.7 - - + +
651C ARG* 1.3 60.2 + - - +
653C VAL* 3.4 3.8 + - - +
654C THR* 2.8 32.2 + - - -
664D PHE* 4.2 5.2 - - - -
665D GLY* 3.6 23.1 - - - +
672D GLN* 3.4 37.8 - - + +
674D SER* 3.8 14.8 - - - -
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Residues in contact with ARG 651 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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647C GLN* 3.2 35.7 + - - +
648C ASP* 4.3 17.0 + - - +
649C ASP 3.4 0.2 - - - -
650C LEU* 1.3 74.8 - - - +
652C LYS* 1.3 59.8 + - + +
654C THR* 3.7 3.2 - - - -
655C GLN* 3.1 50.9 + - + +
680C GLN* 5.2 16.2 - - - +
663D GLN* 4.9 3.2 - - - +
674D SER* 3.8 21.2 + - - +
675D PHE* 4.0 7.1 + - - +
676D ASP* 3.4 50.7 + - - +
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Residues in contact with LYS 652 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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628C THR* 4.1 20.2 - - + +
648C ASP* 3.4 20.6 + - - +
649C ASP* 3.5 8.4 + - - +
650C LEU 3.2 0.6 - - - -
651C ARG* 1.3 76.7 - - + +
653C VAL* 1.3 60.0 + - - +
655C GLN* 3.5 5.0 + - - +
656C SER* 2.9 33.0 + - - -
1I ALA* 3.6 30.7 - - + +
3I ALA 3.7 18.0 + - - -
4I ALA* 3.8 15.2 - - - +
5I ALA 5.0 1.0 - - - +
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Residues in contact with VAL 653 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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625C MET* 3.7 27.7 - - + +
628C THR* 3.9 19.7 - - - -
629C LEU* 3.8 32.3 - - + -
649C ASP 3.2 17.5 + - - +
650C LEU* 3.4 5.1 + - - +
652C LYS* 1.3 72.6 - - - +
654C THR* 1.3 63.6 - - - +
656C SER* 3.6 6.9 + - - -
657C ALA* 3.3 23.0 + - - +
705C ILE* 3.7 27.3 - - + +
672D GLN 4.9 2.2 - - - +
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Residues in contact with THR 654 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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650C LEU 2.8 23.4 + - - -
651C ARG 3.7 4.9 - - - +
652C LYS 3.2 0.2 - - - -
653C VAL* 1.3 77.4 - - - +
655C GLN* 1.3 62.6 + - + +
657C ALA* 3.1 15.4 + - - +
658C TYR* 3.1 30.2 + - + -
705C ILE* 4.4 7.4 - - - -
672D GLN 4.5 0.5 + - - -
673D ILE* 3.3 21.2 - - + +
674D SER 2.8 39.0 + - - +
675D PHE* 3.8 13.7 - - + -
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Residues in contact with GLN 655 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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651C ARG* 3.1 40.9 + - + +
652C LYS* 4.3 4.8 - - - +
654C THR* 1.3 79.9 - - + +
656C SER* 1.3 57.2 + - - +
657C ALA 3.2 1.1 - - - -
658C TYR* 4.1 5.3 - - - +
659C ALA* 3.3 27.0 + - - +
680C GLN* 5.2 17.4 + - - +
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Residues in contact with SER 656 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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621C LEU* 5.6 7.0 - - - -
624C ARG* 6.5 0.7 - - - -
625C MET* 3.4 25.8 - - - +
652C LYS 2.9 21.7 + - - -
653C VAL* 3.6 3.8 + - - -
655C GLN* 1.3 75.2 - - - +
657C ALA* 1.3 56.0 + - - +
659C ALA* 4.5 4.7 - - - +
660C GLN* 2.9 34.8 + - - +
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Residues in contact with ALA 657 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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625C MET* 4.0 3.1 - - + -
653C VAL 3.3 16.5 + - - +
654C THR 3.1 5.1 + - - +
656C SER* 1.3 79.8 - - - +
658C TYR* 1.3 59.6 + - - +
659C ALA 3.6 0.4 - - - -
660C GLN* 4.1 3.1 - - - -
661C ILE* 3.4 30.0 + - - +
701C VAL* 3.6 24.7 - - + +
704C LEU* 3.7 21.6 - - + +
705C ILE* 3.9 10.5 - - + -
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Residues in contact with TYR 658 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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654C THR* 3.1 44.5 + - + +
655C GLN* 4.5 4.9 - - - +
657C ALA* 1.3 76.4 - - - +
659C ALA* 1.3 59.5 + - - +
660C GLN 3.2 1.8 - - - -
661C ILE* 4.9 0.2 - - - -
662C VAL* 2.8 43.1 + - + +
677C LEU* 4.4 16.8 - - + +
689C TYR* 6.1 0.7 - - - -
697C ILE* 4.0 15.3 - - + -
698C ASP* 2.2 37.0 + - - +
701C VAL* 3.7 32.5 - - + +
673D ILE* 4.7 2.9 - - + +
675D PHE* 3.5 25.2 - + - -
688D PRO 4.9 8.5 - - - -
689D TYR* 4.4 2.0 - - - +
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Residues in contact with ALA 659 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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655C GLN 3.3 18.5 + - - +
656C SER* 4.9 3.4 - - - -
658C TYR* 1.3 76.9 - - - +
660C GLN* 1.3 57.2 + - + +
663C GLN* 3.3 17.2 - - + +
664C PHE* 2.7 50.9 + - + -
677C LEU* 4.7 6.2 - - + +
679C ARG* 5.6 5.8 - - - +
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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