Contacts of the helix formed by residues 646 - 662 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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574D HIS* 4.0 18.8 - - + -
632D ARG* 3.8 41.5 - - + +
635D GLU* 4.6 4.7 - - - +
643D THR* 4.4 3.2 + - - +
644D THR* 3.2 1.6 - - - +
645D GLY* 1.3 75.6 - - - +
647D GLN* 1.3 61.2 + - - +
648D ASP 3.5 0.9 - - - -
649D ASP* 3.8 17.3 - - + +
650D LEU* 3.2 26.6 + - + +
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Residues in contact with GLN 647 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
632D ARG* 5.0 0.6 - - - +
644D THR 3.5 14.2 + - - +
645D GLY 3.2 3.8 - - - -
646D ALA* 1.3 77.0 - - - +
648D ASP* 1.3 67.4 + - - +
650D LEU* 3.0 21.4 + - - +
651D ARG* 3.1 27.1 + - - +
663E GLN* 3.0 50.2 + - - +
664E PHE* 3.2 28.6 - - + +
674E SER* 4.2 3.2 + - - +
675E PHE 5.3 0.2 + - - -
7J ALA* 5.3 6.5 - - + +
8J ALA 5.6 2.1 - - - +
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Residues in contact with ASP 648 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
601D LYS* 4.7 8.0 - - - +
645D GLY 4.6 2.0 + - - -
646D ALA 3.5 0.2 - - - -
647D GLN* 1.3 82.4 - - - +
649D ASP* 1.3 66.2 + - - +
650D LEU 3.2 0.2 - - - -
651D ARG* 3.7 28.2 + - - +
652D LYS* 3.6 31.7 + - - +
5J ALA 5.6 3.1 - - - +
7J ALA* 3.3 28.0 - - + +
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Residues in contact with ASP 649 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
574D HIS* 2.8 15.8 + - - -
578D HIS* 3.0 15.7 + - - -
628D THR* 3.3 26.8 - - - +
629D LEU* 5.1 1.3 - - + +
632D ARG 6.1 0.4 - - - +
645D GLY 5.1 0.4 + - - -
646D ALA* 3.6 16.8 + - + +
647D GLN 3.2 0.8 - - - -
648D ASP* 1.3 81.1 - - - +
650D LEU* 1.3 59.2 + - + +
652D LYS* 4.0 3.0 + - - +
653D VAL* 3.3 26.2 + - - +
803D ZN 2.1 36.8 - - - -
4J ALA* 4.4 3.6 - - - +
5J ALA 3.3 11.1 + - - +
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Residues in contact with LEU 650 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
629D LEU* 3.7 27.4 - - + -
632D ARG* 3.4 32.3 - - + +
646D ALA* 3.2 12.5 + - + +
647D GLN* 3.0 9.6 + - - +
649D ASP* 1.3 77.9 - - + +
651D ARG* 1.3 58.8 + - - +
652D LYS 3.3 1.3 - - - -
653D VAL* 3.8 4.9 - - + +
654D THR* 2.9 33.1 + - - -
664E PHE* 4.2 5.2 - - - +
665E GLY* 3.7 23.6 - - - +
672E GLN* 3.4 33.2 - - + +
674E SER* 3.7 15.7 - - - +
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Residues in contact with ARG 651 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
647D GLN* 3.1 24.7 + - - +
648D ASP* 3.7 26.7 + - - +
649D ASP 3.5 0.4 - - - -
650D LEU* 1.3 76.9 - - - +
652D LYS* 1.3 63.6 + - + +
654D THR* 4.1 3.9 - - - -
655D GLN* 3.2 47.8 + - - +
680D GLN* 4.3 24.2 - - - +
457E ASP* 4.2 20.6 + - - +
674E SER* 3.4 28.3 - - - +
675E PHE 4.7 8.3 + - - +
676E ASP* 4.6 17.9 + - - +
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Residues in contact with LYS 652 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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628D THR* 4.4 19.5 - - + +
648D ASP* 3.6 20.3 + - - +
649D ASP* 4.2 6.4 + - - +
650D LEU 3.3 0.6 - - - -
651D ARG* 1.3 78.4 - - + +
653D VAL* 1.3 59.7 + - - +
655D GLN* 3.9 6.0 - - - +
656D SER* 3.0 31.0 + - - -
1J ALA* 4.3 24.3 - - + +
3J ALA 2.5 31.7 + - - +
4J ALA* 4.3 7.3 - - - +
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Residues in contact with VAL 653 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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625D MET* 3.8 23.4 - - + +
628D THR* 4.0 17.9 - - - -
629D LEU* 3.9 26.2 - - + -
649D ASP 3.3 19.9 + - - +
650D LEU* 3.5 7.9 + - + +
651D ARG 3.4 0.2 - - - -
652D LYS* 1.3 73.7 - - - +
654D THR* 1.3 66.0 + - - +
656D SER* 3.5 5.4 + - - -
657D ALA* 3.2 22.7 + - - +
705D ILE* 3.7 37.2 - - + -
672E GLN 4.8 2.2 - - - +
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Residues in contact with THR 654 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
650D LEU 2.9 18.3 + - - -
651D ARG 4.1 3.4 - - - -
652D LYS 3.3 0.2 - - - -
653D VAL* 1.3 77.0 - - - +
655D GLN* 1.3 62.8 + - + +
657D ALA* 3.1 12.4 + - - +
658D TYR* 3.1 26.8 + - + +
701D VAL* 5.1 2.8 - - + +
705D ILE* 4.5 7.6 - - - +
672E GLN 4.5 0.7 + - - -
673E ILE* 3.4 23.6 - - + +
674E SER 3.0 36.8 + - - +
675E PHE* 4.2 14.1 - - + -
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Residues in contact with GLN 655 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
651D ARG* 3.2 40.7 + - - +
652D LYS* 4.2 5.6 - - - +
654D THR* 1.3 80.7 - - + +
656D SER* 1.3 56.7 + - - +
657D ALA 3.2 0.9 - - - -
658D TYR* 4.3 7.6 - - + +
659D ALA* 3.4 25.1 + - - +
677D LEU* 5.0 3.4 - - - +
679D ARG* 5.7 9.1 + - - +
680D GLN* 5.3 10.7 - - - +
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Residues in contact with SER 656 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
621D LEU* 4.8 11.3 + - - +
625D MET* 4.0 18.7 - - - +
652D LYS 3.0 19.3 + - - -
653D VAL 3.5 4.5 + - - -
654D THR 3.2 0.2 - - - -
655D GLN* 1.3 76.2 - - - +
657D ALA* 1.3 57.8 + - - +
659D ALA* 4.2 7.4 - - - +
660D GLN* 3.2 34.6 + - - +
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Residues in contact with ALA 657 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
625D MET* 4.8 1.3 - - + -
653D VAL 3.2 14.5 + - - +
654D THR 3.1 5.2 + - - +
656D SER* 1.3 77.4 - - - +
658D TYR* 1.3 63.7 + - - +
659D ALA 3.2 0.7 - - - -
660D GLN* 3.7 1.5 + - - +
661D ILE* 3.4 30.5 + - - +
701D VAL* 3.8 24.7 - - + -
704D LEU* 3.7 23.6 - - + -
705D ILE* 4.3 8.5 - - + -
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Residues in contact with TYR 658 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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654D THR* 3.1 25.0 + - + +
655D GLN* 4.5 6.3 - - + +
657D ALA* 1.3 74.8 - - - +
659D ALA* 1.3 59.3 + - - +
662D VAL* 2.7 41.0 + - + +
677D LEU* 3.8 28.9 - - + -
697D ILE* 4.0 15.0 - - + -
698D ASP* 2.6 31.9 + - - -
701D VAL* 3.6 26.2 - - + -
675E PHE* 3.3 38.9 - + - -
688E PRO* 3.9 17.9 + - + -
689E TYR* 4.2 0.2 - - - -
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Residues in contact with ALA 659 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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655D GLN 3.4 19.3 + - - +
656D SER* 4.4 6.5 - - - +
657D ALA 3.2 1.0 - - - -
658D TYR* 1.3 79.5 - - - +
660D GLN* 1.3 57.2 + - + +
663D GLN* 3.5 22.7 + - - +
664D PHE* 2.8 48.5 + - + -
677D LEU* 4.1 4.2 - - + +
679D ARG* 5.6 1.6 - - - +
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Residues in contact with GLN 660 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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618D LYS* 5.3 10.1 + - - +
621D LEU* 3.3 45.0 + - + +
622D LEU* 4.7 1.0 - - - +
625D MET* 3.8 15.8 - - - -
656D SER* 3.2 24.4 + - - +
657D ALA 3.7 5.0 + - - +
658D TYR 3.3 0.4 - - - -
659D ALA* 1.3 78.3 - - + +
661D ILE* 1.3 65.3 + - + +
664D PHE* 3.5 8.1 - - + -
666D MET* 2.9 54.1 + - + +
704D LEU* 3.5 24.6 - - + +
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Residues in contact with ILE 661 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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657D ALA 3.4 18.6 + - - +
658D TYR* 3.2 2.3 + - - +
660D GLN* 1.3 83.3 - - + +
662D VAL* 1.3 66.8 + - + +
664D PHE 3.5 8.3 - - - +
665D GLY* 5.1 0.5 - - - -
666D MET 5.6 0.7 - - - +
667D ASN* 3.6 33.5 - - + +
670D VAL* 3.7 29.7 - - + +
671D GLY 5.0 2.8 - - - +
673D ILE 4.1 2.4 - - - +
697D ILE* 4.3 18.8 - - + -
700D GLU* 3.7 37.5 - - + +
701D VAL* 3.8 10.8 - - + -
704D LEU* 4.4 10.5 - - + -
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Residues in contact with VAL 662 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
658D TYR* 2.7 27.7 + - + +
661D ILE* 1.3 73.0 - - + +
663D GLN* 1.3 57.8 + - - +
670D VAL* 5.6 1.6 - - - -
673D ILE 3.1 21.9 - - - +
675D PHE* 3.2 48.9 + - + +
677D LEU* 3.9 27.4 - - + -
689D TYR* 4.6 11.4 - - + +
697D ILE* 3.7 39.5 - - + -
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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
------------------------------------------------------------
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