Contacts of the helix formed by residues 196 - 207 (chain A) in PDB entry 1KEK
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 ASN 196 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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161A ILE* 4.3 5.7 - - + +
162A GLU* 2.9 33.1 + - + +
194A LEU 3.5 2.0 + - - -
195A VAL* 1.3 72.0 - - - +
197A GLN* 1.3 63.8 + - - +
198A LYS* 2.9 30.3 - - - +
199A ALA* 2.8 36.8 + - + +
200A LEU* 3.1 21.5 + - - +
246A TYR* 3.5 16.6 + - - +
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Residues in contact with GLN 197 (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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51A ILE* 6.2 1.0 - - - +
52A PHE* 6.1 0.8 - - - -
192A ALA* 4.3 8.5 + - - +
195A VAL* 3.1 31.2 + - - +
196A ASN* 1.3 70.8 - - - +
198A LYS* 1.3 76.0 + - - +
200A LEU* 3.3 17.7 + - - +
201A ALA* 3.0 23.9 + - - +
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Residues in contact with LYS 198 (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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196A ASN* 2.9 28.7 - - - +
197A GLN* 1.3 92.8 - - - +
199A ALA* 1.3 57.0 + - - +
201A ALA* 3.3 7.7 + - - +
202A GLU* 2.9 42.5 + - + +
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Residues in contact with ALA 199 (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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161A ILE* 3.7 24.0 - - + +
162A GLU* 3.9 15.7 - - + +
164A ASN* 5.9 1.5 + - - +
196A ASN* 2.8 30.3 + - + +
198A LYS* 1.3 75.9 - - - +
200A LEU* 1.3 56.8 + - - +
202A GLU* 3.2 13.9 + - - +
203A PHE* 2.8 29.3 + - - +
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Residues in contact with LEU 200 (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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52A PHE* 3.8 28.9 - - + -
80A LEU* 3.9 29.4 - - + -
161A ILE* 4.2 12.7 - - + +
195A VAL* 4.1 15.0 - - + -
196A ASN 3.1 13.4 + - - +
197A GLN* 3.7 26.0 - - - +
199A ALA* 1.3 77.0 - - - +
201A ALA* 1.4 60.4 + - - +
203A PHE* 3.1 12.0 + - + +
204A ARG* 3.0 48.1 + - - +
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Residues in contact with ALA 201 (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 GLN 3.0 16.3 + - - +
198A LYS* 3.6 7.4 - - - +
200A LEU* 1.4 78.0 - - - +
202A GLU* 1.3 57.7 + - + +
204A ARG* 3.3 10.4 + - - +
205A ALA* 3.0 29.7 + - - +
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Residues in contact with GLU 202 (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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198A LYS* 2.9 29.1 + - - +
199A ALA* 3.7 10.0 - - - +
201A ALA* 1.3 73.9 - - + +
203A PHE* 1.3 66.7 + - - +
205A ALA* 3.8 5.5 - - - +
206A LYS* 3.0 29.0 + - + +
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Residues in contact with PHE 203 (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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75A LEU* 3.5 28.5 - - + -
78A GLY 3.5 30.5 - - - -
79A ALA 3.8 18.6 - - - -
80A LEU* 3.9 21.1 - - + -
105A LEU* 4.4 4.7 - - + -
106A PRO* 3.4 38.6 - - + -
161A ILE* 5.7 4.5 - - + +
164A ASN* 4.9 5.4 - - - +
199A ALA 2.8 13.6 + - - +
200A LEU* 3.1 19.0 + - + +
202A GLU* 1.3 79.1 - - - +
204A ARG* 1.3 63.4 + - + +
206A LYS* 3.4 25.7 - - - +
207A SER* 2.8 22.3 + - - -
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Residues in contact with ARG 204 (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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23A GLU* 2.7 42.0 + - - -
52A PHE* 3.6 28.1 - - - -
78A GLY 2.8 28.9 + - - +
79A ALA* 4.0 1.2 - - - +
80A LEU 4.3 2.0 - - - +
200A LEU* 3.0 41.4 + - - +
201A ALA* 3.3 9.8 + - - +
203A PHE* 1.3 80.0 - - + +
205A ALA* 1.3 63.4 + - - +
207A SER* 3.2 20.0 + - - +
212A HIS* 4.6 4.2 + - - -
886B ARG* 3.9 35.5 + - - +
889B HIS* 5.7 2.2 + - - -
950B ASP* 4.8 4.4 - - - +
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Residues in contact with ALA 205 (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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201A ALA 3.0 17.0 + - - +
202A GLU* 4.0 6.7 - - - +
203A PHE 3.3 0.2 - - - -
204A ARG* 1.3 79.2 - - - +
206A LYS* 1.3 59.2 + - - +
212A HIS* 3.6 25.4 + - - -
950B ASP* 5.7 0.9 - - - -
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Residues in contact with LYS 206 (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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103A GLU 4.4 4.8 + - - -
104A LEU* 2.9 31.5 + - - +
105A LEU* 4.9 7.6 - - + -
164A ASN* 3.1 28.4 + - - +
202A GLU 3.0 15.5 + - - +
203A PHE* 3.4 29.6 - - - +
205A ALA* 1.3 75.8 - - - +
207A SER* 1.3 68.6 + - - +
212A HIS* 5.6 0.2 - - - -
214A HIS* 3.5 2.8 + - - -
216A ARG* 4.6 0.3 + - - -
662B ASP* 4.6 6.3 + - - +
664B ARG* 3.0 47.5 + - - +
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Residues in contact with SER 207 (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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75A LEU 4.1 3.5 + - - -
76A ALA 3.5 5.6 + - - -
77A ALA 3.8 2.9 - - - -
78A GLY* 3.1 37.6 + - - -
105A LEU* 5.9 0.5 - - - +
203A PHE* 2.8 19.8 + - - -
204A ARG 3.2 12.5 + - - -
206A LYS* 1.3 85.3 - - - +
208A MET* 1.3 69.1 + - - +
209A ASN* 3.3 2.3 + - - -
212A HIS* 3.8 17.0 + - - +
214A HIS* 3.9 4.2 + - - -
216A ARG* 5.2 1.6 - - - +
886B ARG* 4.7 2.9 - - - -
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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