Contacts of the strand formed by residues 226 - 231 (chain A) in PDB entry 1KYZ
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 LYS 226 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202A LYS* 2.7 44.0 + - - +
203A SER* 3.3 23.7 - - - -
204A LEU 3.4 1.2 + - - -
223A PRO 3.8 13.5 + - - -
224A THR 4.0 8.3 - - - -
225A ILE* 1.3 81.0 - - - +
227A GLY* 1.3 61.7 + - - +
228A ILE* 3.9 6.5 + - - +
244A GLY* 4.1 20.2 - - - +
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Residues in contact with GLY 227 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204A LEU 3.2 11.0 - - - -
215A ILE* 3.7 22.7 - - - -
219A VAL* 3.8 5.3 - - - +
225A ILE* 3.2 9.9 + - - -
226A LYS* 1.3 75.7 - - - +
228A ILE* 1.3 62.5 + - - +
244A GLY 3.3 7.0 + - - +
245A VAL* 3.4 5.8 - - - -
246A GLU* 3.1 22.7 + - - +
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Residues in contact with ILE 228 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203A SER* 5.7 2.7 - - - -
204A LEU 2.8 13.3 + - - +
205A VAL* 4.2 17.0 - - + -
206A ASP* 2.9 29.6 + - - +
215A ILE* 3.9 4.1 - - - +
226A LYS 4.3 7.9 - - - +
227A GLY* 1.3 76.4 - - - +
229A ASN* 1.3 63.4 + - - +
230A PHE 3.4 2.3 + - - +
246A GLU* 3.3 22.0 - - - +
248A VAL* 3.3 35.7 - - + -
257A PRO* 4.1 19.7 - - + -
258A LYS* 4.2 13.5 - - - +
259A ALA* 5.2 3.8 - - + -
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Residues in contact with ASN 229 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206A ASP* 4.2 1.5 + - - -
209A GLY* 3.0 39.2 + - - +
210A GLY 3.2 7.4 + - - +
211A THR 3.1 4.0 - - - -
212A GLY* 2.9 29.4 + - - -
215A ILE* 4.1 14.5 - - + +
227A GLY 4.3 0.4 - - - -
228A ILE* 1.3 70.0 - - - +
230A PHE* 1.3 62.0 + - - +
231A ASP 3.8 0.5 + - - -
236A ILE* 3.4 5.8 - - - +
245A VAL* 4.2 3.4 - - + +
246A GLU 3.0 8.1 + - - -
247A HIS* 3.0 31.6 + - + +
248A VAL 2.9 24.8 + - - +
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Residues in contact with PHE 230 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205A VAL* 3.7 20.2 - - + -
206A ASP 3.3 10.5 + - - +
207A VAL* 4.5 11.7 - - + -
208A GLY 2.9 28.3 + - - -
209A GLY 3.3 2.9 + - - -
228A ILE* 3.4 2.1 + - + -
229A ASN* 1.3 71.1 - - - +
231A ASP* 1.3 62.6 + - - +
248A VAL* 3.1 16.8 - - + -
249A GLY 4.1 1.3 - - - -
250A GLY* 3.4 27.1 - - - -
251A ASP 3.6 16.8 - - - -
252A MET* 3.7 15.0 - - + -
255A SER 3.3 18.6 - - - -
256A ILE* 3.6 30.7 - - + -
257A PRO* 3.6 28.9 - - + -
1698A SAH 4.8 2.4 + + - -
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Residues in contact with ASP 231 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208A GLY* 3.1 27.4 - - - -
210A GLY* 3.5 18.3 + - - +
229A ASN 3.8 1.4 + - - -
230A PHE* 1.3 74.7 - - - +
232A LEU* 1.3 70.1 + - - +
235A VAL* 2.9 26.0 - - - +
236A ILE* 3.6 19.0 - - + +
248A VAL 3.2 4.9 + - - -
249A GLY* 3.1 6.4 - - - -
250A GLY 3.0 24.2 + - - -
1698A SAH 2.7 39.5 + - - -
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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