Contacts of the helix formed by residues 207 - 214 (chain A) in PDB entry 3K6R
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 PHE 207 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132A MSE 3.8 7.7 - - + +
133A PHE* 3.6 20.6 - + + -
183A ASP* 5.7 2.9 - - - -
184A ASN* 3.5 33.4 - - - -
185A ARG* 3.5 38.4 - - + +
198A MSE 3.8 13.9 - - + -
200A TYR* 3.9 26.2 - + - -
202A VAL 4.6 0.9 - - - -
203A ARG 4.5 7.4 - - - -
204A THR* 3.0 19.5 + - - +
206A GLU* 1.3 88.7 - - + +
208A ILE* 1.3 63.5 + - - +
209A PRO* 3.4 2.5 - - - -
210A LYS* 3.3 9.0 + - + +
211A ALA* 3.1 18.2 + - - +
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Residues in contact with ILE 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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198A MSE 4.3 1.8 - - + -
204A THR 3.8 0.4 + - - +
205A HIS* 3.2 34.1 - - + +
207A PHE* 1.3 76.1 - - - +
209A PRO* 1.4 68.8 - - + +
211A ALA* 3.1 9.2 + - + +
212A LEU* 2.9 42.9 + - + +
223A TYR* 4.1 7.2 - - + +
240A PHE* 3.4 56.1 - - + -
243A ILE* 3.8 22.7 - - + -
244A THR* 3.9 10.8 - - - +
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Residues in contact with PRO 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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205A HIS 4.0 4.3 - - - +
206A GLU 3.7 12.3 - - - +
207A PHE 3.5 4.0 - - - -
208A ILE* 1.4 93.3 - - + +
210A LYS* 1.3 60.9 + - - +
212A LEU* 3.5 12.8 + - + +
213A SER* 3.3 21.1 + - - -
243A ILE* 4.5 3.4 - - + -
247A TYR* 3.4 51.2 - - + +
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Residues in contact with LYS 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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132A MSE 4.0 14.6 - - + -
184A ASN 3.4 24.0 - - - +
185A ARG* 3.4 33.9 + - + +
187A PHE 2.8 28.9 + - - -
188A PRO* 4.8 2.6 - - - +
189A GLY 4.8 2.6 + - - -
207A PHE* 3.3 11.5 + - + +
208A ILE 3.2 0.4 - - - -
209A PRO* 1.3 76.1 - - - +
211A ALA* 1.3 66.5 + - - +
213A SER* 3.2 17.4 + - - -
214A ILE* 3.0 38.7 + - + +
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Residues in contact with ALA 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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132A MSE 3.8 19.8 - - - +
196A ILE* 3.2 15.2 - - + +
198A MSE 3.7 29.8 - - - -
207A PHE 3.1 8.3 + - - +
208A ILE* 3.1 10.2 + - + +
210A LYS* 1.3 76.3 - - - +
212A LEU* 1.3 56.4 + - - +
214A ILE* 3.3 2.5 + - - +
215A ALA* 2.9 26.8 + - - +
221A ILE* 4.1 14.8 - - + -
240A PHE* 6.1 0.2 - - + -
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Residues in contact with LEU 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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208A ILE* 2.9 40.1 + - + +
209A PRO* 3.7 7.0 - - + +
211A ALA* 1.3 75.2 - - + +
213A SER* 1.3 61.6 + - - +
215A ALA* 3.6 16.6 + - - +
221A ILE* 4.7 4.7 - - + -
240A PHE* 5.1 0.7 - - + -
243A ILE 5.0 0.4 - - - +
244A THR* 4.0 27.4 - - - +
247A TYR* 4.3 13.7 - - + -
249A TYR* 3.1 61.3 + - + -
275A VAL* 3.9 30.5 - - + -
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Residues in contact with SER 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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189A GLY 4.7 2.6 + - - -
190A GLU* 3.5 24.9 + - - +
191A ASN* 2.8 31.0 + - - +
209A PRO 3.3 10.7 + - - -
210A LYS* 3.2 22.5 + - - -
212A LEU* 1.3 78.2 - - - +
214A ILE* 1.3 52.8 + - - +
215A ALA 3.5 0.5 + - - +
249A TYR* 4.7 3.9 + - - -
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Residues in contact with ILE 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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130A VAL* 3.7 31.9 - - + -
132A MSE 4.2 26.0 - - + -
154A ILE* 5.1 1.1 - - + -
184A ASN 4.8 2.9 - - - +
187A PHE* 3.9 21.3 - - + -
189A GLY 3.5 21.1 - - - +
191A ASN 4.0 0.4 - - - +
192A ILE* 2.8 36.5 + - + +
193A ALA* 3.0 14.8 + - + -
196A ILE* 3.9 7.6 - - + -
210A LYS* 3.0 38.3 + - + +
211A ALA 3.7 5.6 - - - +
213A SER* 1.3 76.8 - - - +
215A ALA* 1.3 54.3 + - - +
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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