Contacts of the helix formed by residues 632 - 640 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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646A ALA* 3.9 18.8 - - + +
649A PHE* 3.5 25.4 - - + -
650A SER* 4.3 3.4 + - - -
630B TRP 3.7 2.2 + - - -
631B MET* 1.3 73.5 - - - +
633B PRO* 1.3 70.2 - - + +
634B GLU* 3.6 22.7 - - - +
635B VAL* 2.9 24.4 + - + +
636B PHE* 2.9 11.4 + - - +
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Residues in contact with PRO 633 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
637A THR* 4.7 0.4 - - - -
649A PHE* 3.4 35.7 - - + -
674A ASP 5.7 0.4 - - - +
677A MET* 4.3 12.3 - - + +
678A ALA* 4.0 26.7 - - + +
683A ARG* 4.2 11.4 - - - +
704A ALA* 5.1 9.2 - - + +
709A ARG* 4.2 3.1 - - - +
631B MET 3.6 2.2 - - - +
632B ALA* 1.3 87.2 - - + +
634B GLU* 1.3 62.1 + - - +
636B PHE* 3.4 5.1 + - + +
637B THR* 3.1 32.6 + - - -
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Residues in contact with GLU 634 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
637A THR* 3.1 30.5 - - + +
640A THR* 6.0 6.1 - - + +
641A ARG 5.3 7.6 - - - +
642A TYR* 6.0 0.9 - - - -
643A THR* 4.7 3.4 + - - +
646A ALA* 3.9 10.8 + - + +
704A ALA 4.5 1.7 - - - +
706A PRO* 3.7 20.3 - - + +
709A ARG* 2.9 44.4 + - - -
632B ALA* 3.6 12.7 - - - +
633B PRO* 1.3 75.6 - - - +
635B VAL* 1.3 69.3 + - + +
638B GLN* 3.1 31.4 + - - +
679B TYR* 5.5 6.7 - - + +
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Residues in contact with VAL 635 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
587A ARG* 6.2 0.2 - - - +
642A TYR* 3.3 48.5 - - + -
646A ALA* 3.8 16.8 - - + -
631B MET* 3.8 25.4 - - + -
632B ALA* 2.9 16.4 + - + +
634B GLU* 1.3 82.1 - - + +
636B PHE* 1.3 65.9 + - - +
637B THR 3.2 0.2 - - - -
638B GLN* 2.9 20.9 + - + +
639B CYS* 3.3 16.2 + - - -
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Residues in contact with PHE 636 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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671A ALA* 4.0 18.2 - - + -
674A ASP* 3.4 32.5 - - + +
675A MET* 4.1 10.3 - - + -
678A ALA* 4.0 17.9 - - + -
679A TYR* 3.8 33.0 - + - -
628B LEU* 4.0 24.9 - - + -
631B MET* 3.4 15.3 - - + +
632B ALA 2.9 12.4 + - - +
633B PRO* 3.7 10.1 - - + +
635B VAL* 1.3 74.6 - - - +
637B THR* 1.3 63.6 + - - +
639B CYS* 3.2 6.1 + - + +
640B THR* 2.9 40.5 + - + -
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Residues in contact with THR 637 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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634A GLU* 3.0 41.9 - - + +
637A THR* 3.6 29.8 - - + +
638A GLN* 3.6 12.5 + - + +
678A ALA* 4.8 5.0 - - - +
679A TYR* 4.6 10.8 - - - -
633B PRO 3.1 15.3 + - - -
634B GLU 3.9 0.4 - - - -
636B PHE* 1.3 82.7 - - - +
638B GLN* 1.3 58.9 + - - +
640B THR* 3.4 23.1 + - - +
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Residues in contact with GLN 638 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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637A THR 3.7 2.0 - - - +
638A GLN* 3.6 41.2 + - + +
640A THR 2.7 28.6 + - - +
641A ARG* 4.0 16.9 - - - +
642A TYR* 4.2 6.5 + - - +
634B GLU* 3.1 24.2 + - - +
635B VAL* 2.9 13.5 + - + +
637B THR* 1.3 74.3 - - - +
639B CYS* 1.3 62.4 + - - +
640B THR 3.2 6.1 + - - +
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Residues in contact with CYS 639 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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628B LEU* 5.7 4.0 - - + -
631B MET* 3.8 24.5 - - + -
635B VAL* 3.7 16.6 - - - -
636B PHE* 3.2 8.4 + - + +
638B GLN* 1.3 77.9 - - - +
640B THR* 1.3 58.5 + - - +
641B ARG 4.1 0.5 + - - -
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Residues in contact with THR 640 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
638A GLN* 3.3 22.3 + - - -
679A TYR* 3.8 19.3 - - - +
636B PHE* 2.9 42.9 + - + -
637B THR* 3.4 10.2 - - - +
638B GLN 3.2 1.5 - - - +
639B CYS* 1.3 81.4 - - - +
641B ARG* 1.3 77.0 + - + +
643B THR* 5.9 1.6 - - + -
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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