Contacts of the helix formed by residues 629 - 634 (chain J) in PDB entry 1O1F
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 GLU 629 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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257 ASP* 3.2 2.9 - - - +
625J THR* 3.5 24.6 + - - +
626J TYR* 3.5 6.1 + - - +
628J GLY* 1.4 66.5 - - - +
630J ALA* 1.3 65.5 + - - +
631J GLU 3.1 3.4 - - - -
632J GLY* 3.1 4.7 + - - -
633J GLY 3.8 0.7 + - - -
640J LYS 4.1 2.6 - - - +
643J GLY* 1.9 36.3 + - - +
644J SER* 0.7 144.1 - - - +
645J SER* 1.3 77.4 + - - +
646J PHE* 4.5 8.4 + - - -
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Residues in contact with ALA 630 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257 ASP* 1.5 50.9 - - - +
605J GLU* 6.0 2.7 - - - +
626J TYR 3.6 10.3 + - - +
627J GLY* 4.1 13.5 - - - +
628J GLY 3.5 1.4 - - - -
629J GLU* 1.3 70.9 - - - +
631J GLU* 1.3 52.1 + - + +
634J GLY* 3.9 1.0 - - - -
645J SER* 6.0 0.4 - - - -
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Residues in contact with GLU 631 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247 ASP* 3.9 4.0 - - + +
257 ASP* 2.7 15.6 + - - +
267 ALA* 2.7 26.2 + - - +
287 ARG* 4.6 19.2 + - - +
627J GLY 5.3 2.7 - - - +
628J GLY* 4.3 19.9 - - - +
629J GLU 3.0 2.2 + - - +
630J ALA* 1.3 76.7 - - + +
632J GLY* 1.3 50.9 + - - +
634J GLY* 4.2 0.3 - - - -
643J GLY* 4.9 3.0 - - - -
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Residues in contact with GLY 632 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237 GLY 2.9 3.4 - - - -
247 ASP* 0.6 201.7 - - - +
257 ASP* 0.9 68.8 - - - +
629J GLU 3.1 4.2 + - - -
631J GLU* 1.3 70.7 - - - +
633J GLY* 1.3 33.3 - - - +
643J GLY* 3.1 6.3 - - - -
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Residues in contact with GLY 633 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237 GLY 3.5 5.2 + - - -
247 ASP 3.2 1.6 - - - -
257 ASP* 1.2 97.3 + - - +
3417 ILE* 5.6 2.7 - - - -
629J GLU 3.8 0.4 + - - -
632J GLY* 1.3 65.5 - - - -
634J GLY* 1.3 61.0 + - - +
635J GLY 3.4 9.8 + - - +
639J GLY 4.0 6.7 - - - -
640J LYS* 4.8 6.7 + - - -
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Residues in contact with GLY 634 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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257 ASP* 1.2 84.7 - - - +
267 ALA* 3.9 6.3 - - - -
3347 GLU* 4.1 2.1 - - - +
407J GLY* 3.4 14.2 - - - +
410J ASN* 5.5 2.0 - - - -
411J GLU 4.8 2.6 - - - +
630J ALA 3.9 1.6 - - - -
631J GLU 4.2 1.1 - - - -
633J GLY 1.3 36.2 - - - +
635J GLY* 1.3 55.1 + - - -
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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