Contacts of the helix formed by residues 618 - 629 (chain E) 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 LYS 618 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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641D ARG* 5.5 0.6 - - - +
642D ILE* 3.4 20.6 + - + +
617E THR* 1.3 77.7 - - - +
619E GLU* 1.3 66.6 + - - +
621E LEU* 3.4 7.4 + - - +
622E LEU* 3.3 21.0 + - + +
660E GLN* 5.0 9.8 + - - +
666E MET* 3.1 56.8 + - + +
667E ASN* 5.3 0.6 - - - +
668E GLU 5.9 0.2 - - - +
704E LEU* 6.0 6.1 - - - -
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Residues in contact with GLU 619 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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641D ARG* 3.3 36.2 + - - +
587E HIS* 4.0 18.7 + - + +
617E THR* 4.2 2.9 - - - +
618E LYS* 1.3 81.3 + - - +
620E GLN* 1.3 63.1 + - - +
621E LEU 3.2 1.1 - - - -
622E LEU* 3.9 17.9 - - + -
623E ASP* 3.0 31.2 + - - +
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Residues in contact with GLN 620 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
641D ARG* 5.6 2.4 - - - +
587E HIS* 3.5 50.1 + - + +
611E LYS* 6.1 1.4 - - - +
613E GLN* 2.7 44.7 + - - +
615E LEU 3.7 2.9 + - - +
616E TYR* 3.8 3.8 - - + -
617E THR* 3.2 42.9 + - - +
618E LYS 3.3 1.2 - - - -
619E GLU* 1.3 78.3 - - - +
621E LEU* 1.3 59.8 + - - +
623E ASP 4.3 1.8 - - - -
624E ARG* 3.3 26.2 + - - +
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Residues in contact with LEU 621 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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644D THR* 4.4 13.2 - - + -
616E TYR* 3.7 37.7 - - + -
617E THR 3.7 14.4 - - - +
618E LYS 3.4 6.4 + - - +
619E GLU 3.2 0.2 - - - -
620E GLN* 1.3 77.7 - - - +
622E LEU* 1.3 63.3 + - - +
623E ASP 3.3 1.3 - - - -
624E ARG* 3.2 23.7 + - + +
625E MET* 3.1 25.6 + - - +
656E SER* 4.6 11.6 + - - +
660E GLN* 3.3 37.9 - - + +
664E PHE* 4.8 6.5 - - + -
666E MET* 4.8 4.7 - - + -
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Residues in contact with LEU 622 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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618E LYS 3.3 14.9 + - - +
619E GLU* 4.1 15.7 - - + +
621E LEU* 1.3 77.5 - - - +
623E ASP* 1.3 58.6 + - - +
625E MET* 3.3 25.6 + - + +
626E CYS* 3.1 38.7 + - - -
660E GLN* 4.7 1.2 - - - +
704E LEU* 4.7 12.3 - - + +
707E ASP* 5.0 5.6 - - + +
708E ALA* 3.8 22.0 - - + +
711E ARG* 4.3 24.0 - - - +
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Residues in contact with ASP 623 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
585E LEU* 3.6 36.8 - - + +
586E GLU* 4.4 3.3 + - - +
587E HIS* 3.5 45.7 + - + +
588E ALA* 4.1 6.7 - - - +
619E GLU* 3.0 22.7 + - - +
620E GLN 4.7 0.9 - - - +
621E LEU 3.3 0.6 - - - -
622E LEU* 1.3 79.2 - - - +
624E ARG* 1.3 58.8 + - - +
626E CYS* 4.0 1.7 - - - +
627E MET* 3.3 20.8 + - - +
711E ARG* 3.8 21.3 + - - -
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Residues in contact with ARG 624 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
587E HIS 4.4 9.2 - - - +
588E ALA* 5.1 4.3 - - - +
589E ASP* 2.8 41.2 + - - +
610E PRO* 4.7 9.7 - - - +
611E LYS 5.5 0.2 - - - +
613E GLN* 6.3 0.2 - - - +
616E TYR* 5.0 20.9 + - - -
620E GLN 3.3 20.6 - - - +
621E LEU* 3.2 25.2 + - + +
622E LEU 3.2 1.0 - - - -
623E ASP* 1.3 78.7 - - - +
625E MET* 1.3 56.9 + - - +
626E CYS 3.3 0.2 - - - -
627E MET* 3.7 15.5 + - + +
628E THR* 2.6 33.1 + - - -
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Residues in contact with MET 625 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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621E LEU 3.1 11.4 + - - +
622E LEU* 3.3 35.8 + - + +
624E ARG* 1.3 76.2 - - - +
626E CYS* 1.3 54.3 + - - +
628E THR* 2.9 6.6 + - - -
629E LEU* 2.7 40.7 + - + +
652E LYS 5.9 0.2 - - - -
653E VAL* 3.9 43.7 - - + +
656E SER* 4.5 17.3 - - - +
657E ALA* 4.6 2.0 - - - -
660E GLN* 4.3 9.6 - - - +
704E LEU* 3.8 31.2 - - + -
705E ILE* 4.7 4.0 - - - -
708E ALA* 4.1 14.4 - - + -
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Residues in contact with CYS 626 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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581E ALA* 4.2 3.6 - - - +
585E LEU* 3.7 22.7 - - + -
622E LEU* 3.1 22.9 + - - +
623E ASP* 4.4 0.4 - - - -
624E ARG 3.3 0.2 - - - -
625E MET* 1.3 76.7 - - - +
627E MET* 1.3 61.1 + - - +
629E LEU* 4.5 0.2 - - - -
630E GLY* 3.3 6.2 + - - -
708E ALA* 3.4 30.3 - - - -
711E ARG* 3.7 32.3 - - + -
712E THR* 3.3 38.1 - - + +
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Residues in contact with MET 627 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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578E HIS* 2.8 33.3 + - - +
581E ALA* 4.7 5.4 - - - -
582E GLY* 3.7 28.0 - - - -
585E LEU* 4.0 4.6 - - + +
588E ALA* 4.6 6.3 - - + -
589E ASP* 4.4 23.8 - - + +
608E TYR* 3.1 46.0 - - + -
623E ASP 3.3 17.4 + - - +
624E ARG* 4.0 18.4 - - + +
625E MET 3.2 0.2 - - - -
626E CYS* 1.3 78.8 - - - +
628E THR* 1.3 65.5 + - - +
630E GLY 3.5 4.5 + - - -
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Residues in contact with THR 628 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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578E HIS* 3.1 22.3 - - + -
624E ARG 2.6 20.2 + - - -
625E MET 2.9 7.2 + - - -
627E MET* 1.3 83.2 - - - +
629E LEU* 1.3 61.7 + - - +
630E GLY 3.2 1.8 - - - -
631E GLY* 3.9 1.0 + - - -
632E ARG* 4.8 1.6 + - - +
649E ASP* 3.3 48.1 - - + +
652E LYS* 4.5 18.4 - - + +
653E VAL* 3.9 12.8 - - + -
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Residues in contact with LEU 629 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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625E MET 2.7 20.7 + - - +
626E CYS 4.0 0.4 - - - -
627E MET 3.4 0.2 - - - -
628E THR* 1.3 70.8 - - - +
630E GLY* 1.3 62.0 + - - +
631E GLY 3.3 0.7 - - - -
632E ARG* 3.1 12.3 + - + +
633E VAL* 3.1 25.8 + - + +
650E LEU* 3.7 30.3 - - + -
653E VAL* 4.0 16.2 - - + -
705E ILE* 3.9 14.4 - - + +
708E ALA* 3.5 41.5 - - + +
709E TYR* 3.7 19.7 - - + +
712E THR* 4.0 14.6 - - - +
672F GLN* 4.9 2.7 - - + +
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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