Contacts of the strand formed by residues 207 - 214 (chain A) in PDB entry 1K9A
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 GLY 207 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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204A GLY* 3.0 27.4 + - - +
205A GLU 3.6 1.6 - - - -
206A PHE* 1.3 79.4 - - - +
208A ASP* 1.3 64.7 + - - +
209A VAL* 5.4 2.6 - - - +
222A LYS* 5.2 8.3 - - - -
223A CYS 3.1 14.1 - - - -
224A ILE* 4.3 0.2 - - - -
225A LYS* 3.9 11.5 - - - +
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Residues in contact with ASP 208 (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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200A THR* 5.4 1.6 - - + -
202A GLY 3.5 4.0 - - - +
203A LYS* 3.2 33.2 - - + +
207A GLY* 1.3 72.8 - - - +
209A VAL* 1.3 67.3 + - - +
210A MET* 4.7 10.9 - - + +
221A VAL 3.7 0.7 - - - +
222A LYS* 3.2 6.9 - - - +
223A CYS* 3.0 47.0 + - - -
225A LYS* 2.9 38.4 + - - -
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Residues in contact with VAL 209 (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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200A THR* 3.6 1.4 - - - +
201A ILE* 2.7 48.3 + - + -
202A GLY* 2.9 22.2 + - - +
207A GLY 5.4 1.3 - - - +
208A ASP* 1.3 80.4 - - - +
210A MET* 1.3 64.9 + - - +
220A ALA* 4.5 13.0 - - + -
221A VAL 3.3 8.3 - - - +
222A LYS* 4.6 16.4 - - + -
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Residues in contact with MET 210 (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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197A LEU* 4.5 25.6 - - + -
199A GLN 3.1 11.2 - - - +
200A THR* 3.8 22.2 - - + +
201A ILE* 3.7 5.5 - - - +
208A ASP* 4.7 12.3 - - + +
209A VAL* 1.3 80.7 - - - +
211A LEU* 1.3 66.5 + - - +
212A GLY 3.7 0.2 + - - -
220A ALA* 3.5 4.0 - - - -
221A VAL* 2.8 55.9 + - + +
223A CYS* 4.7 9.4 - - + -
263A TYR* 3.9 31.0 - - + -
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Residues in contact with LEU 211 (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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197A LEU* 4.0 1.2 - - - -
198A LEU* 3.0 36.5 + - + -
199A GLN* 2.7 42.5 + - + +
201A ILE* 3.4 20.4 - - + +
210A MET* 1.3 76.4 - - - +
212A GLY* 1.3 73.4 + - - +
218A LYS* 4.1 28.0 - - + +
219A VAL 3.6 6.3 - - - +
221A VAL* 5.4 0.2 - - - -
268A TYR* 3.6 38.4 - - + +
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Residues in contact with GLY 212 (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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195A LEU* 4.4 9.6 - - - -
196A LYS 3.4 11.4 - - - -
197A LEU* 4.5 1.1 - - - -
198A LEU* 4.1 8.9 - - - +
210A MET 3.7 0.8 + - - -
211A LEU* 1.3 80.1 - - - +
213A ASP* 1.3 61.1 + - - +
218A LYS* 3.2 8.1 - - - -
219A VAL* 2.7 40.0 + - - -
221A VAL* 4.8 2.7 - - - -
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Residues in contact with ASP 213 (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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194A GLU 3.2 4.2 - - - +
195A LEU* 3.4 3.6 - - - +
196A LYS* 2.9 46.4 + - + +
198A LEU* 4.3 15.6 - - + +
212A GLY* 1.3 74.7 - - - +
214A TYR* 1.3 59.6 + - - +
215A ARG 4.0 1.7 + - - -
216A GLY* 3.2 37.9 + - - +
217A ASN 3.4 5.0 - - - +
218A LYS* 5.0 1.9 + - + +
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Residues in contact with TYR 214 (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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33A GLY* 6.1 1.3 - - - -
190A LEU* 3.4 38.8 - - + +
191A ASN* 3.0 43.0 + - - +
194A GLU* 3.3 17.0 - - + -
195A LEU* 3.7 15.7 - - + -
212A GLY 4.2 0.4 - - - -
213A ASP* 1.3 73.4 + - - +
215A ARG* 1.3 112.1 + - + +
216A GLY 3.1 0.4 - - - -
217A ASN* 2.9 28.5 + - - +
219A VAL* 4.4 22.8 - - + +
252A LEU* 6.5 0.4 - - + -
255A ILE* 4.7 1.8 - - + -
265A VAL* 5.2 5.8 - - + -
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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