Contacts of the helix formed by residues 617 - 629 (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 THR 617 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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641C ARG* 4.3 21.9 - - + +
642C ILE 3.4 11.4 - - - -
643C THR* 3.9 18.8 - - + -
615D LEU* 4.2 7.0 - - + +
616D TYR* 1.3 79.3 - - - +
618D LYS* 1.3 65.1 + - - +
619D GLU* 3.4 13.7 + - - +
620D GLN* 3.3 38.1 + - - +
621D LEU* 3.4 24.8 + - - +
666D MET* 4.0 2.9 - - - -
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Residues in contact with LYS 618 (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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641C ARG* 6.0 0.9 - - - -
642C ILE* 3.4 31.4 + - + +
617D THR* 1.3 76.9 - - - +
619D GLU* 1.3 71.9 + - + +
621D LEU* 3.7 3.9 + - - +
622D LEU* 3.4 20.6 + - - +
660D GLN* 5.3 9.1 + - - +
666D MET* 3.6 41.7 + - + +
667D ASN* 5.7 0.4 - - - +
668D GLU* 5.9 5.3 - - - +
704D LEU* 6.1 4.9 - - - -
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Residues in contact with GLU 619 (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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640C GLY 4.9 3.5 - - - +
641C ARG* 3.4 37.7 - - - +
587D HIS* 4.4 16.4 - - + +
617D THR* 3.6 5.4 + - - +
618D LYS* 1.3 85.5 + - + +
620D GLN* 1.3 63.3 + - - +
621D LEU 3.1 2.2 - - - -
622D LEU* 3.3 9.5 + - + +
623D ASP* 3.1 31.7 + - - +
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Residues in contact with GLN 620 (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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567C GLU* 4.9 2.8 + - - -
587D HIS* 3.5 49.0 + - + +
613D GLN* 2.8 39.2 + - - +
615D LEU 3.6 12.5 + - - +
616D TYR* 3.7 6.7 - - + -
617D THR* 3.3 32.7 + - - +
618D LYS 3.4 0.2 - - - -
619D GLU* 1.3 76.0 - - - +
621D LEU* 1.3 59.8 + - - +
623D ASP 4.2 1.5 - - - -
624D ARG* 3.3 29.2 + - - +
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Residues in contact with LEU 621 (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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644C THR* 4.0 23.1 - - + -
616D TYR* 3.9 29.2 - - + -
617D THR 3.4 18.7 + - - +
618D LYS 4.1 2.9 - - - +
619D GLU 3.1 0.8 - - - -
620D GLN* 1.3 80.0 - - - +
622D LEU* 1.3 62.9 + - - +
623D ASP 3.4 0.2 - - - -
624D ARG* 3.5 15.2 + - + +
625D MET* 3.2 27.4 + - - +
656D SER* 4.8 9.2 + - - +
660D GLN* 3.3 37.0 - - + +
664D PHE* 4.8 6.7 - - + -
666D MET* 4.3 7.0 - - + -
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Residues in contact with LEU 622 (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 3.4 14.6 + - - +
619D GLU* 3.3 11.8 + - + +
621D LEU* 1.3 78.3 - - - +
623D ASP* 1.3 53.2 + - - +
625D MET* 3.0 12.0 + - + +
626D CYS* 2.7 56.3 + - - -
660D GLN* 4.7 0.8 - - - +
704D LEU* 5.3 9.0 - - + +
707D ASP* 5.1 2.0 - - + +
708D ALA* 3.9 23.8 - - + +
711D ARG* 3.8 27.1 - - - +
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Residues in contact with ASP 623 (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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585D LEU* 3.6 22.3 - - + +
586D GLU* 4.3 3.5 + - - +
587D HIS* 3.4 37.3 + - + +
588D ALA* 4.0 23.0 - - - +
619D GLU* 3.1 15.6 + - - +
620D GLN 4.6 0.9 - - - +
622D LEU* 1.3 76.8 - - - +
624D ARG* 1.3 60.4 + - - +
626D CYS* 4.0 1.1 - - - -
627D MET* 3.4 21.7 + - - +
711D ARG* 2.9 36.3 + - - -
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Residues in contact with ARG 624 (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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587D HIS 4.6 10.1 - - - +
588D ALA* 5.2 4.5 - - - +
589D ASP* 3.0 36.5 + - - +
610D PRO* 5.1 5.7 - - - +
611D LYS 5.3 1.2 + - - +
613D GLN* 6.2 0.7 - - - +
616D TYR* 4.8 26.7 + - - -
620D GLN 3.3 19.4 + - - +
621D LEU* 3.5 21.7 + - + +
622D LEU 3.2 0.8 - - - -
623D ASP* 1.3 78.2 - - - +
625D MET* 1.3 62.0 + - + +
627D MET* 3.7 13.7 + - + +
628D THR* 2.8 27.0 + - - -
1J ALA* 3.2 44.7 + - - +
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Residues in contact with MET 625 (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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621D LEU 3.2 11.5 + - - +
622D LEU* 3.0 14.1 + - - +
624D ARG* 1.3 75.3 - - + +
626D CYS* 1.3 59.3 + - - +
627D MET 3.1 1.8 - - - -
628D THR* 3.2 5.8 + - - +
629D LEU* 2.9 35.6 + - - +
653D VAL* 3.8 34.3 - - + +
656D SER* 4.0 24.0 - - - +
657D ALA* 4.8 0.2 - - + -
660D GLN* 3.8 24.0 - - - -
704D LEU* 4.3 18.6 - - + -
705D ILE* 4.2 13.9 - - + -
708D ALA* 4.0 22.2 - - + -
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Residues in contact with CYS 626 (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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581D ALA* 4.1 4.3 - - - +
585D LEU* 3.7 14.8 - - + +
622D LEU* 2.7 37.8 + - - +
625D MET* 1.3 73.4 - - - +
627D MET* 1.3 58.9 + - - +
629D LEU 4.2 0.7 - - - -
630D GLY* 3.5 5.0 + - - -
708D ALA* 3.7 19.7 - - - -
711D ARG* 3.1 42.0 - - + +
712D THR* 3.2 36.3 + - + +
715D LEU* 5.9 1.1 - - + -
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Residues in contact with MET 627 (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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577D GLY 4.6 0.3 - - - +
578D HIS* 3.3 25.7 + - - +
581D ALA* 4.5 7.0 - - - -
582D GLY* 3.8 31.4 - - - +
585D LEU* 4.0 3.1 - - + +
588D ALA* 4.7 4.3 - - + -
589D ASP* 4.9 15.5 - - - +
608D TYR* 3.1 47.3 - - + +
623D ASP 3.4 17.3 + - - +
624D ARG* 3.9 13.0 - - + +
625D MET 3.1 0.8 - - - -
626D CYS* 1.3 77.4 - - - +
628D THR* 1.3 72.7 + - - +
630D GLY* 3.4 9.0 + - - -
1J ALA* 5.6 6.5 - - + +
4J ALA* 5.1 3.8 - - + -
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Residues in contact with THR 628 (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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578D HIS* 3.3 21.9 - - + -
624D ARG 2.8 18.0 + - - -
625D MET* 3.2 5.3 + - - -
627D MET* 1.3 85.2 - - - +
629D LEU* 1.3 63.9 + - - +
631D GLY 3.8 1.6 + - - -
632D ARG 5.0 0.5 + - - -
649D ASP* 3.3 48.7 - - + +
652D LYS* 4.4 20.3 - - + +
653D VAL* 4.0 9.9 - - + -
4J ALA* 5.7 3.4 - - + -
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Residues in contact with LEU 629 (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 2.9 15.2 + - - +
626D CYS 4.3 0.2 - - - -
628D THR* 1.3 72.7 - - - +
630D GLY* 1.3 63.1 - - - +
631D GLY 3.1 4.8 + - - -
632D ARG* 3.4 11.6 + - + +
633D VAL* 3.3 26.7 + - + +
649D ASP* 5.1 1.3 - - + +
650D LEU* 3.7 29.6 - - + -
653D VAL* 3.9 18.2 - - + -
705D ILE* 4.0 18.4 - - + +
708D ALA* 3.8 29.8 - - + +
709D TYR* 3.9 26.6 - - + +
712D THR* 4.5 9.0 - - - +
672E GLN* 4.9 2.5 - - + +
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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
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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