Contacts of the helix formed by residues 256 - 260 (chain I) in PDB entry 3KDO
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 VAL 256 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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254I VAL* 3.8 16.2 - - + +
255I ASP* 1.3 73.2 - - - +
257I VAL* 1.3 63.1 + - - +
259I THR* 3.7 6.5 - - - -
260I GLY* 3.2 21.5 + - - +
264I LEU* 4.0 15.7 - - + +
280I GLY* 3.8 13.9 - - - -
281I HIS 2.8 26.7 + - - +
282I ARG* 4.3 4.5 - - - -
305I TYR* 3.6 38.7 + - + -
310I ILE* 3.9 26.9 - - + -
313I LEU* 4.4 6.7 - - + -
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Residues in contact with VAL 257 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260E GLY* 5.7 0.3 - - - -
261E TRP* 5.3 1.6 - - - -
255I ASP 3.4 0.4 - - - -
256I VAL* 1.3 78.1 - - - +
258I ILE* 1.3 64.2 + - - +
260I GLY* 3.5 10.2 + - - -
281I HIS 3.9 0.6 + - - -
282I ARG* 3.5 27.4 - - + +
283I ALA 3.5 17.7 - - - +
284I MET* 4.1 12.6 - - + +
285I HIS* 3.9 20.9 - - + +
288I PHE* 4.1 21.1 - - + -
301I LEU* 4.3 8.5 - - + -
305I TYR* 3.3 21.8 - - + +
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Residues in contact with ILE 258 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102E PRO* 3.7 35.0 - - + +
105E LEU* 3.7 8.1 - - + +
106E ALA* 3.1 45.5 - - + +
109E ALA 5.1 0.2 - - - +
260E GLY* 4.6 0.2 - - - -
261E TRP* 3.3 33.8 + - + +
231I THR* 4.7 4.7 - - + -
255I ASP* 3.4 12.8 + - + +
257I VAL* 1.3 75.6 - - - +
259I THR* 1.3 68.7 + - - +
260I GLY 3.3 0.3 + - - -
283I ALA* 3.7 24.4 + - + +
284I MET* 3.9 19.7 - - + -
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Residues in contact with THR 259 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102E PRO* 6.1 1.1 - - - -
259E THR 4.1 1.9 - - - +
260E GLY 3.7 1.6 - - - -
261E TRP 3.6 1.6 + - - -
262E GLY* 2.6 42.1 + - - +
263E ALA 4.3 0.2 + - - -
231I THR* 4.8 5.4 + - - +
237I MET* 4.3 22.2 - - + -
254I VAL* 3.3 20.0 - - + +
255I ASP* 2.7 25.5 + - - +
256I VAL* 3.7 5.6 - - - -
257I VAL 3.4 0.2 - - - -
258I ILE* 1.3 77.6 - - - +
260I GLY* 1.3 65.4 + - - +
263I ALA* 4.8 6.5 + - + -
264I LEU* 4.4 20.4 - - + +
267I ILE* 4.8 3.1 - - + -
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Residues in contact with GLY 260 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258E ILE 4.5 0.7 - - - -
260E GLY* 3.7 17.0 - - - -
256I VAL 3.2 10.7 + - - -
257I VAL 3.5 9.2 + - - -
258I ILE 3.2 1.4 - - - -
259I THR* 1.3 82.6 - - - +
261I TRP* 1.3 69.1 + - - -
262I GLY 3.3 2.9 + - - -
263I ALA 3.8 0.5 + - - -
264I LEU* 3.3 24.7 + - - +
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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