Contacts of the helix formed by residues 196 - 204 (chain B) in PDB entry 1K7E
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 PRO 196 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5B LEU* 5.8 0.4 - - + -
25B LEU* 3.9 21.5 - - + +
28B LEU* 3.9 13.9 - - + -
29B GLU* 3.8 27.6 - - + +
32B PHE* 5.4 2.0 - - + -
194B PRO 4.3 0.2 - - - +
195B HIS* 1.3 108.8 - - + +
197B TYR* 1.3 63.3 + - + +
198B PRO* 3.5 2.5 - - - -
199B THR* 3.1 6.3 + - + -
200B ILE* 2.7 52.7 + - + +
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Residues in contact with TYR 197 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25B LEU* 4.0 18.2 - - + -
28B LEU* 3.4 32.1 - - + +
94B GLN* 3.6 22.7 - - - -
177B TRP* 3.5 19.9 - + - -
185B HIS* 3.5 3.1 - - - -
186B TYR* 2.6 32.9 + + - +
188B LEU* 3.6 33.4 - - + -
192B ALA 3.5 12.8 - - - +
194B PRO* 3.1 27.5 + - + +
196B PRO* 1.3 80.6 - - + +
198B PRO* 1.3 68.9 - - + +
200B ILE* 4.4 7.6 - - + +
201B VAL* 2.9 31.8 + - + +
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Residues in contact with PRO 198 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9B PHE* 4.0 16.2 - - + -
191B ALA* 3.7 26.8 - - + +
192B ALA* 3.7 10.8 - - - +
193B GLY 3.4 16.2 - - - +
194B PRO 3.5 12.1 - - - +
195B HIS* 3.9 5.6 - - + +
196B PRO 3.7 2.7 - - - -
197B TYR* 1.3 96.0 - - + +
199B THR* 1.3 60.4 + - - +
202B ARG* 3.4 20.8 + - - +
311B PRO* 3.7 26.7 - - + -
312B GLN* 4.7 6.0 - - + +
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Residues in contact with THR 199 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5B LEU* 4.3 17.3 - - + -
6B ASN 4.9 2.1 + - - -
9B PHE* 3.6 20.1 - - - -
32B PHE* 4.0 21.1 - - + -
195B HIS* 4.1 16.6 + - + -
196B PRO* 3.1 8.9 + - + -
197B TYR 3.0 0.6 - - - -
198B PRO* 1.3 78.3 - - - +
200B ILE* 1.3 68.3 + - + +
202B ARG* 3.4 28.2 + - - +
203B GLU* 2.9 28.4 + - + +
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Residues in contact with ILE 200 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28B LEU* 3.9 19.5 - - + -
32B PHE* 3.4 48.2 - - + -
94B GLN* 4.8 9.6 - - + -
97B LEU* 4.3 4.5 - - + -
196B PRO* 2.7 49.0 + - + +
197B TYR* 3.9 6.5 - - + +
199B THR* 1.3 73.8 - - - +
201B VAL* 1.3 59.4 + - + +
203B GLU* 3.0 1.4 + - - +
204B PHE* 2.9 56.8 + - + +
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Residues in contact with VAL 201 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90B GLN* 3.6 36.8 - - + +
94B GLN* 4.1 12.3 - - - +
188B LEU 4.5 1.1 - - - +
190B THR* 3.4 25.1 - - - +
191B ALA* 3.8 8.1 - - + +
197B TYR* 2.9 26.9 + - + +
200B ILE* 1.3 77.2 - - + +
202B ARG* 1.3 60.8 + - - +
204B PHE* 3.4 3.5 + - - +
205B GLN* 3.2 24.0 + - + +
235B SER* 3.7 30.3 - - - -
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Residues in contact with ARG 202 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9B PHE* 3.6 18.8 - - - -
198B PRO 3.4 18.3 + - - +
199B THR* 3.4 24.4 + - - +
201B VAL* 1.3 75.2 - - - +
203B GLU* 1.3 95.0 + - - +
205B GLN* 3.0 2.1 + - - +
206B ARG* 2.9 34.2 + - - +
238B ILE* 3.7 33.8 - - + +
239B GLY* 4.8 0.5 - - - -
242B ALA* 4.0 22.9 - - + -
245B ILE* 5.8 0.2 - - - -
312B GLN* 2.8 47.4 + - - +
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Residues in contact with GLU 203 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32B PHE* 3.8 28.3 - - + -
36B GLN* 4.1 16.2 + - - +
45B PHE* 5.4 0.7 - - - -
199B THR* 2.9 22.4 + - + +
200B ILE 3.0 1.1 + - - +
202B ARG* 1.3 118.9 + - - +
204B PHE* 1.4 61.9 + - - +
205B GLN 3.2 0.2 - - - -
206B ARG* 2.9 53.3 + - - +
207B MET* 4.6 3.6 - - - +
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Residues in contact with PHE 204 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32B PHE* 4.0 11.4 - + - -
36B GLN* 3.4 25.4 - - - -
41B PHE* 4.0 23.1 - + - -
42B GLN* 6.1 0.2 - - - -
45B PHE* 3.8 23.3 - + + -
89B ASN* 3.4 16.5 - - - +
90B GLN* 3.8 22.0 - - + -
93B GLY* 3.3 33.7 - - - -
94B GLN* 3.5 8.1 - - + -
97B LEU* 3.6 26.7 - - + -
200B ILE* 2.9 27.2 + - + +
201B VAL 4.1 0.2 - - - +
202B ARG 3.2 0.2 - - - -
203B GLU* 1.4 84.2 - - + +
205B GLN* 1.3 59.0 + - - +
206B ARG 3.5 0.2 - - - -
207B MET* 3.3 17.9 - - - +
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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