Contacts of the helix formed by residues 637 - 641 (chain E) in PDB entry 3E20
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 TYR 637 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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468E PRO* 3.1 33.9 - - + +
470E ILE* 3.9 19.7 - - + -
489E GLU* 4.7 5.6 - - + -
490E ALA* 4.0 21.3 - - + -
632E GLU* 3.8 26.0 - - + -
633E ARG 3.1 6.9 + - - +
634E PHE 3.6 2.0 - - - -
636E ASP* 1.3 97.4 - - + +
638E GLN* 1.3 67.3 + - - +
639E TYR* 3.2 3.4 - - + +
640E MET* 3.1 20.0 + - + +
641E GLY* 3.0 16.5 + - - -
634J PHE* 6.3 1.1 - + - -
638J GLN* 3.6 8.5 - - - -
642J ARG* 5.8 5.2 - - - -
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Residues in contact with GLN 638 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
634E PHE* 3.2 54.2 + - + +
637E TYR* 1.3 71.3 - - - +
639E TYR* 1.3 57.7 + - - +
641E GLY 2.7 17.2 + - - -
642E ARG* 2.9 26.7 + - - +
634J PHE 5.3 0.2 + - - -
635J GLU 5.1 2.4 + - - -
636J ASP 2.9 28.5 + - - -
637J TYR* 3.5 6.8 - - - +
638J GLN* 2.6 55.7 + - + +
639J TYR 4.3 1.0 + - - -
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Residues in contact with TYR 639 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
472E PRO* 4.3 7.4 - - + -
489E GLU* 3.3 54.4 + - + +
583E ILE 3.9 15.3 - - - +
584E HIS* 3.7 31.3 - - + +
585E THR* 4.1 7.6 + - - -
637E TYR* 3.2 1.4 + - + -
638E GLN* 1.3 79.1 - - - +
640E MET* 1.3 68.0 + - + +
642E ARG* 4.0 16.4 + - - +
487J LYS* 4.3 23.0 + - - -
489J GLU* 6.1 1.3 - - - -
638J GLN* 4.3 1.4 + - - -
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Residues in contact with MET 640 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
470E ILE* 3.7 29.2 - - + -
472E PRO* 3.9 16.6 - - + -
489E GLU* 4.8 6.5 - - + -
546E VAL* 4.3 6.7 - - + -
554E VAL* 4.0 19.3 - - + -
583E ILE* 3.6 18.6 - - - +
584E HIS* 3.4 36.6 - - + -
631E MET* 3.9 7.2 - - - +
632E GLU* 3.6 36.3 + - + +
637E TYR* 3.1 18.4 + - + +
639E TYR* 1.3 86.1 - - + +
641E GLY* 1.3 60.1 + - - +
642E ARG 3.6 0.9 - - - -
657E VAL* 4.1 0.9 - - - +
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Residues in contact with GLY 641 (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 GLU 3.2 16.8 - - - -
634E PHE* 3.6 16.8 - - - -
637E TYR 3.0 4.2 + - - -
638E GLN 2.7 9.4 + - - -
640E MET* 1.3 78.5 - - - +
642E ARG* 1.3 60.7 + - - -
643E PHE* 4.0 0.3 - - - -
655E GLY 3.8 0.2 - - - +
656E LYS* 3.1 6.4 - - - -
657E VAL* 2.9 33.2 + - - +
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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