Contacts of the helix formed by residues 632 - 637 (chain C) in PDB entry 4YFI
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 ALA 632 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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630C TRP 3.8 1.0 + - - -
631C MET* 1.3 74.3 - - - +
633C PRO* 1.4 62.1 - - + +
634C GLU* 3.5 27.8 - - - +
635C VAL* 2.7 30.3 + - + +
636C PHE* 3.0 11.0 + - - +
646D ALA* 3.8 28.3 - - + +
649D PHE* 3.6 12.7 - - + -
650D SER* 4.2 3.4 + - - -
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Residues in contact with PRO 633 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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631C MET 3.7 1.3 - - - +
632C ALA* 1.4 85.2 - - + +
634C GLU* 1.3 64.2 + - - +
636C PHE* 3.6 6.0 + - + +
637C THR* 3.3 27.5 + - - -
649D PHE* 3.4 36.1 - - + -
674D ASP 5.5 0.2 - - - +
677D MET* 4.5 4.0 - - + +
678D ALA* 3.7 36.8 - - + +
683D ARG* 4.3 11.0 - - - +
704D ALA* 5.1 7.4 - - + +
709D ARG* 3.9 4.3 - - - +
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Residues in contact with GLU 634 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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632C ALA* 3.5 9.8 - - - +
633C PRO* 1.3 78.4 - - - +
635C VAL* 1.3 61.1 + - + +
637C THR* 4.6 0.2 - - - -
638C GLN* 3.5 12.5 + - - +
679C TYR* 4.2 18.2 - - + +
637D THR* 2.9 42.9 - - + +
642D TYR* 6.6 0.4 - - - -
643D THR* 4.4 6.2 + - - +
646D ALA* 3.6 19.4 + - - +
704D ALA 4.5 1.6 - - - +
706D PRO* 3.8 16.6 - - + +
709D ARG* 3.0 43.6 + - - -
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Residues in contact with VAL 635 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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631C MET* 4.0 21.3 - - + -
632C ALA* 2.7 25.7 + - + +
634C GLU* 1.3 78.0 - - + +
636C PHE* 1.3 64.8 + - - +
637C THR 3.1 2.0 - - - -
638C GLN* 3.1 22.2 + - - +
639C CYS* 3.6 8.4 - - - -
587D ARG* 5.4 7.6 - - - +
642D TYR* 3.3 48.0 - - + +
646D ALA* 3.6 18.6 - - + -
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Residues in contact with PHE 636 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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628C LEU* 4.0 24.2 - - + -
631C MET* 3.6 18.6 - - + +
632C ALA 3.0 9.7 + - - +
633C PRO* 3.7 10.1 - - + +
635C VAL* 1.3 76.2 - - - +
637C THR* 1.3 67.4 + - - +
639C CYS* 3.2 21.9 + - + +
640C THR* 4.1 11.2 + - - -
671D ALA* 4.3 11.9 - - + -
674D ASP* 3.2 37.2 - - + +
675D MET* 4.0 19.7 - - + -
678D ALA* 4.1 10.8 - - + -
679D TYR* 3.6 33.2 - + - -
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Residues in contact with THR 637 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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633C PRO 3.3 15.0 + - - -
634C GLU* 4.6 0.2 - - - -
635C VAL 3.1 0.4 - - - -
636C PHE* 1.3 88.7 - - - +
638C GLN* 1.3 59.6 + - - +
639C CYS 3.2 1.0 + - - -
640C THR* 3.4 16.1 + - - +
633D PRO 4.8 0.2 - - - -
634D GLU* 3.2 44.5 - - + +
637D THR* 3.3 26.9 - - + +
638D GLN* 3.4 12.0 - - - +
678D ALA* 5.0 1.9 - - - +
679D TYR* 4.4 13.6 + - - -
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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