Contacts of the helix formed by residues 632 - 641 (chain B) in PDB entry 5YPO
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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540B LEU* 3.8 26.3 - - + +
631B SER* 1.3 76.2 + - - +
633B ASN* 1.3 61.2 + - - +
635B VAL* 3.0 23.9 + - + +
636B ARG 4.3 1.0 + - - -
680B LEU* 3.6 31.2 - - + -
684B PHE* 3.7 29.1 - - + -
687B CYS* 5.3 0.7 - - - -
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Residues in contact with ASN 633 (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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631B SER* 2.9 14.6 + - - +
632B ALA* 1.3 77.3 - - - +
634B ALA* 1.3 62.2 + - - +
635B VAL 3.3 0.7 + - - -
636B ARG* 3.6 11.9 + - - +
637B ARG* 3.5 39.7 + - - +
683B GLU* 4.9 1.9 - - - +
684B PHE* 3.1 30.0 - - - -
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Residues in contact with ALA 634 (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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538B ILE* 4.3 2.7 - - + -
599B ILE* 3.5 33.8 - - + +
600B GLU* 4.3 5.1 + - - +
630B VAL* 3.5 27.8 - - + -
631B SER* 2.9 16.2 + - - +
633B ASN* 1.3 77.0 - - - +
635B VAL* 1.3 57.1 + - - +
636B ARG 3.4 0.2 - - - -
637B ARG* 3.1 4.1 + - - +
638B LEU* 2.8 31.7 + - - +
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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
----------------------------------------------------------
538B ILE* 3.6 27.8 - - + -
540B LEU* 4.6 3.8 - - + -
632B ALA* 3.0 23.4 + - - +
634B ALA* 1.3 77.4 - - - +
636B ARG* 1.3 64.6 + - - +
638B LEU* 3.1 4.4 + - - +
639B GLN* 3.0 45.1 + - - +
645B PRO* 4.1 6.0 - - + +
647B ALA* 4.0 20.0 - - + -
687B CYS* 3.7 33.4 - - + +
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Residues in contact with ARG 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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632B ALA 4.3 1.2 + - - +
633B ASN* 3.6 9.2 + - - +
634B ALA 3.4 0.2 - - - -
635B VAL* 1.3 79.2 - - - +
637B ARG* 1.3 59.7 + - + +
639B GLN* 3.8 11.8 - - - +
640B ALA* 2.9 30.0 + - - +
687B CYS* 5.3 4.6 - - + +
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Residues in contact with ARG 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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596B HIS* 6.6 0.4 - - - -
598B PHE 3.9 9.4 - - - +
599B ILE* 2.4 54.3 + - - +
600B GLU* 3.6 13.8 + - - +
601B ALA 5.3 4.0 + - - +
613B VAL* 5.5 0.8 - - + +
633B ASN* 3.5 42.7 + - - +
634B ALA 3.1 7.5 + - - +
636B ARG* 1.3 77.5 - - + +
638B LEU* 1.3 57.8 + - - +
640B ALA* 3.3 6.6 + - - +
641B ALA* 2.9 30.1 + - - +
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Residues in contact with LEU 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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536B PRO* 4.6 2.7 - - + -
538B ILE* 3.5 33.0 - - + -
599B ILE* 3.7 27.3 - - + +
616B VAL* 4.0 15.0 - - + -
628B LEU* 3.6 17.0 - - + -
634B ALA 2.8 11.1 + - - +
635B VAL 3.6 6.5 - - - +
637B ARG* 1.3 75.6 - - - +
639B GLN* 1.3 62.0 + - - +
641B ALA* 3.2 10.3 + - - +
643B LEU* 3.0 52.5 + - + +
645B PRO* 3.8 24.9 - - + -
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Residues in contact with GLN 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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635B VAL* 3.0 40.6 + - - +
636B ARG* 3.8 9.5 - - - +
638B LEU* 1.3 74.4 - - - +
640B ALA* 1.3 59.1 + - - +
642B HIS* 2.8 26.7 + - - -
644B HIS* 4.7 3.6 - - - +
645B PRO* 3.5 25.2 + - + +
647B ALA* 5.7 0.2 - - - +
687B CYS* 3.9 17.5 + - - +
689B SER* 5.8 1.2 + - - -
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Residues in contact with ALA 640 (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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636B ARG 2.9 18.2 + - - +
637B ARG* 3.8 7.2 - - - +
639B GLN* 1.3 76.3 - - - +
641B ALA* 1.3 57.4 + - - +
642B HIS* 3.2 17.8 + - - -
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Residues in contact with ALA 641 (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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596B HIS 5.9 0.2 - - - +
599B ILE* 5.6 0.2 - - + -
613B VAL* 4.0 34.1 - - + -
617B ARG* 4.4 8.4 + - - +
637B ARG 2.9 17.2 + - - +
638B LEU* 3.7 7.2 - - - +
639B GLN 3.1 0.6 - - - -
640B ALA* 1.3 75.2 - - - +
642B HIS* 1.3 71.2 + - - +
643B LEU* 3.3 16.2 + - + +
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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