Contacts of the helix formed by residues 637 - 641 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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467D ALA* 4.8 1.9 + - - -
468D PRO* 3.1 33.8 - - + +
470D ILE* 4.3 11.0 - - + -
489D GLU 5.4 2.0 - - - -
490D ALA* 4.1 24.2 - - + -
632D GLU* 3.6 33.7 - - + -
633D ARG 3.0 8.7 + - - +
634D PHE 3.9 2.2 - - - -
636D ASP* 1.3 92.8 - - + +
638D GLN* 1.3 68.5 + - - +
639D TYR* 3.2 1.8 - - + +
640D MET* 2.9 32.5 + - + +
641D GLY* 3.1 8.1 + - - -
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Residues in contact with GLN 638 (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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634D PHE* 3.4 47.7 + - + +
636D ASP 4.1 0.4 - - - -
637D TYR* 1.3 70.4 - - - +
639D TYR* 1.3 63.3 + - - +
641D GLY 3.1 1.2 + - - -
642D ARG* 3.0 46.0 + - - +
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Residues in contact with TYR 639 (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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472D PRO* 4.3 5.6 - - + -
487D LYS* 6.0 1.6 - - - -
489D GLU* 3.2 50.7 - - + +
583D ILE 4.1 9.9 - - - +
584D HIS* 3.6 37.1 - - + +
585D THR* 4.0 5.7 + - - -
637D TYR* 3.0 1.8 + - + +
638D GLN* 1.3 79.4 - - - +
640D MET* 1.3 66.7 + - + +
641D GLY 3.0 4.0 + - - -
642D ARG* 3.8 24.6 + - + +
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Residues in contact with MET 640 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
470D ILE* 3.8 32.8 - - + -
472D PRO* 4.2 8.1 - - + -
489D GLU* 4.7 5.6 - - + -
546D VAL* 4.4 7.4 - - + -
554D VAL* 4.1 17.9 - - + -
583D ILE* 4.0 8.5 - - - +
584D HIS* 3.5 36.3 - - + +
630D CYS 4.7 2.7 - - - +
631D MET* 3.6 13.1 - - - +
632D GLU* 3.0 41.4 + - + +
637D TYR* 2.9 20.3 + - + +
639D TYR* 1.3 92.1 - - + +
641D GLY* 1.3 56.5 + - - +
657D VAL* 4.0 0.2 - - - +
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Residues in contact with GLY 641 (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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632D GLU 3.2 16.2 - - - -
634D PHE* 3.9 16.6 - - - -
637D TYR 3.1 2.2 + - - -
638D GLN 3.1 5.8 + - - -
639D TYR 3.0 0.6 - - - -
640D MET* 1.3 80.2 - - - +
642D ARG* 1.3 65.6 + - - +
643D PHE* 3.6 1.4 - - - -
656D LYS* 3.1 4.9 - - - -
657D VAL* 3.0 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
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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