Contacts of the helix formed by residues 629 - 638 (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 LEU 629 (chain E).
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Specific contacts
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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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Residues in contact with GLY 630 (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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577E GLY* 3.5 23.6 - - - -
581E ALA* 4.6 0.4 - - - -
626E CYS 3.3 9.8 + - - -
627E MET 3.5 3.6 + - - -
628E THR 3.2 3.0 - - - -
629E LEU* 1.3 77.9 - - - +
631E GLY* 1.3 56.8 + - - +
634E SER* 3.1 31.5 + - - -
712E THR* 3.7 18.6 - - - -
716E LEU* 3.6 4.0 - - - +
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Residues in contact with GLY 631 (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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574E HIS* 2.6 61.2 + - - -
578E HIS* 3.5 15.8 + - - -
629E LEU 3.3 1.0 - - - -
630E GLY* 1.3 76.3 - - - +
632E ARG* 1.3 58.2 + - - +
634E SER* 4.3 1.6 - - - -
635E GLU* 3.6 15.1 + - - +
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Residues in contact with ARG 632 (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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574E HIS* 4.2 0.6 - - - -
628E THR 4.8 1.7 + - - +
629E LEU* 3.1 19.9 + - + +
631E GLY* 1.3 76.2 - - - +
633E VAL* 1.3 63.2 + - - +
634E SER 3.4 0.4 - - - -
635E GLU* 4.0 9.5 + - - +
636E GLU* 3.4 23.2 + - - +
642E ILE* 3.3 45.6 - - - +
643E THR 4.9 6.8 + - - -
646E ALA* 4.1 25.0 - - + +
649E ASP* 6.3 0.4 - - + +
650E LEU* 3.4 33.0 - - + +
709E TYR* 4.4 13.4 + - + -
665F GLY* 3.2 35.7 + - - +
666F MET* 3.5 1.6 - - - +
672F GLN* 3.3 21.3 + - - +
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Residues in contact with VAL 633 (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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629E LEU 3.1 16.0 + - - +
630E GLY 3.5 0.4 + - - -
632E ARG* 1.3 75.2 - - - +
634E SER* 1.3 60.0 + - - +
636E GLU* 3.1 8.8 + - + +
637E ILE* 2.9 44.7 + - + +
709E TYR* 3.8 25.1 - - + -
712E THR* 3.9 19.1 - - + +
713E VAL* 3.7 36.6 - - + -
716E LEU* 3.8 17.5 - - + -
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Residues in contact with SER 634 (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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573E TYR 2.7 26.2 + - - -
577E GLY* 3.6 11.0 - - - -
630E GLY 3.1 19.0 + - - -
631E GLY 4.7 1.6 - - - -
632E ARG 3.4 0.2 - - - -
633E VAL* 1.3 78.1 - - - +
635E GLU* 1.3 57.0 + - - +
637E ILE* 3.5 5.5 + - - +
638E PHE* 3.2 35.8 + - - -
716E LEU* 4.1 8.9 - - - +
723E VAL* 3.4 22.5 - - - +
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Residues in contact with GLU 635 (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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570E THR* 3.4 28.1 - - - +
573E TYR* 4.8 4.9 - - + -
574E HIS* 3.7 15.1 + - - +
631E GLY 3.6 20.9 + - - +
632E ARG* 4.0 12.9 - - - +
634E SER* 1.3 78.6 - - - +
636E GLU* 1.3 57.0 + - - +
638E PHE* 4.7 0.4 - - - -
639E PHE* 3.3 45.0 - - + +
640E GLY 3.8 0.2 + - - -
641E ARG 3.6 11.7 - - - +
642E ILE* 4.7 4.3 - - + -
643E THR* 2.9 37.8 + - - -
646E ALA* 4.8 4.3 + - - +
615F LEU* 5.6 1.2 - - - +
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Residues in contact with GLU 636 (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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632E ARG* 3.4 20.4 + - - +
633E VAL* 3.1 6.8 + - - +
634E SER 3.1 0.8 - - - -
635E GLU* 1.3 78.7 - - - +
637E ILE* 1.3 62.8 + - + +
638E PHE 3.4 0.9 - - - -
640E GLY* 2.8 34.4 + - - +
642E ILE* 4.1 23.0 - - + +
709E TYR* 2.3 31.7 + - - -
713E VAL* 5.8 0.8 - - - +
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Residues in contact with ILE 637 (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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633E VAL* 2.9 39.4 + - + +
634E SER* 4.0 4.7 - - - +
636E GLU* 1.3 80.5 - - + +
638E PHE* 1.3 63.5 + - + +
639E PHE 3.5 0.5 + - - -
640E GLY 4.8 0.3 + - - -
713E VAL* 4.7 6.1 - - + +
716E LEU* 4.0 9.0 - - + +
717E THR* 3.8 39.7 - - - +
720E LYS* 3.8 41.3 + - + +
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Residues in contact with PHE 638 (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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573E TYR* 3.4 49.8 - + + -
634E SER* 3.2 19.8 + - - +
637E ILE* 1.3 81.2 - - + +
639E PHE* 1.3 79.7 + - + +
720E LYS* 3.5 50.3 - - + +
723E VAL* 3.6 31.0 - - + -
724E GLU* 4.0 15.7 - - + -
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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