Contacts of the strand formed by residues 251 - 255 (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 HIS 251 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146I VAL* 4.6 5.6 - - + -
149I MET* 3.6 29.7 - - + -
150I LEU* 5.3 0.9 - - + -
225I THR* 2.9 26.8 + - + +
226I TRP 3.5 26.8 + - - +
227I PHE* 3.6 27.4 - + + -
228I ALA* 4.0 2.8 + - - +
244I LEU* 3.3 20.1 - - - +
249I LEU* 3.8 1.5 - - - +
250I LYS* 1.3 82.2 + - - +
252I ALA* 1.3 59.0 + - - +
253I MET 4.2 0.2 - - - -
276I LEU* 4.1 4.1 - - - +
277I ALA* 3.3 24.1 - - + +
278I ILE 4.6 0.2 - - - -
279I HIS* 4.7 4.7 - - + -
312I GLN* 2.6 36.5 + - - -
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Residues in contact with ALA 252 (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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228I ALA 3.9 3.4 - - - -
230I ILE* 4.5 6.1 - - + -
241I LEU* 3.5 32.3 - - + -
244I LEU* 3.9 8.3 - - + -
251I HIS* 1.3 74.6 - - - +
253I MET* 1.3 60.7 + - - +
254I VAL* 4.6 2.9 - - + -
271I ALA* 4.9 5.8 - - + -
276I LEU* 4.4 8.7 - - + +
277I ALA 2.8 12.9 + - - +
278I ILE* 3.3 9.6 - - + +
279I HIS* 2.9 24.5 + - - -
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Residues in contact with MET 253 (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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189I KCX 3.6 24.7 - - - +
190I ASP 3.3 28.0 - - - +
192I GLU* 3.5 29.4 - - + -
227I PHE* 3.7 22.7 - - + +
228I ALA 2.7 22.9 + - - +
229I ASN* 3.5 17.2 - - - +
230I ILE* 3.1 28.1 + - - +
252I ALA* 1.3 71.9 - - - +
254I VAL* 1.3 68.1 + - - +
255I ASP* 3.6 12.1 - - - +
279I HIS* 3.3 16.6 - - + +
281I HIS* 4.1 5.8 - - + -
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Residues in contact with VAL 254 (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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230I ILE* 4.0 22.9 - - + -
231I THR* 4.0 3.1 - - - +
237I MET* 5.1 3.4 - - - -
252I ALA* 4.3 4.9 - - + +
253I MET* 1.3 81.3 - - - +
255I ASP* 1.3 69.4 + - - +
256I VAL* 3.1 17.5 + - + +
259I THR* 3.3 27.1 - - + +
264I LEU* 4.4 9.0 - - + -
267I ILE* 4.2 15.5 - - + -
278I ILE* 4.1 19.5 - - + -
279I HIS 2.8 9.2 + - - +
280I GLY* 3.5 1.9 - - - -
281I HIS* 2.8 25.7 + - - +
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Residues in contact with ASP 255 (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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106E ALA* 3.4 16.1 - - - +
192I GLU* 2.9 30.3 - - - +
229I ASN* 4.2 0.2 - - - -
231I THR* 2.9 33.0 + - + +
253I MET* 3.6 15.6 - - - +
254I VAL* 1.3 68.2 - - - +
256I VAL* 1.3 56.4 + - - +
257I VAL 3.4 2.5 - - - -
258I ILE* 3.4 15.1 + - + -
259I THR* 2.7 35.1 + - - -
281I HIS* 3.3 25.8 - - - +
283I ALA* 5.0 3.6 - - + +
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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