Contacts of the helix formed by residues 170 - 181 (chain B) in PDB entry 1KFV
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 170 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2B GLU* 2.7 24.5 + - - +
57B LYS* 3.6 1.1 - - - -
161B LEU* 3.5 8.7 - - - -
168B GLY 3.4 1.0 + - - -
169B LEU* 1.3 74.7 - - - +
171B ASN* 1.3 65.2 + - - -
174B VAL* 3.0 23.0 + - - +
8G T 2.9 23.6 - - - -
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Residues in contact with ASN 171 (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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2B GLU* 3.8 1.2 + - - -
157B LYS* 2.9 29.1 + - - -
161B LEU* 3.9 8.2 - - - +
170B GLY* 1.3 71.0 - - - -
172B ILE* 1.3 65.2 + - - +
174B VAL* 4.1 1.1 - - - +
175B ASP* 3.5 21.0 + - - +
238B TYR* 3.4 14.2 - - - -
260B ARG* 3.2 32.1 + - - +
261B GLY* 3.1 22.6 + - - +
263B HIS* 4.9 0.4 - - - -
6G T 5.3 0.6 + - - -
7G PDI 2.7 31.8 + - - +
8G T 3.0 13.1 + - - +
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Residues in contact with ILE 172 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2B GLU* 2.8 21.9 + - - +
5B GLU* 5.4 3.8 - - - +
171B ASN* 1.3 79.7 - - - +
173B TYR* 1.3 69.6 + - + +
175B ASP* 3.2 3.8 + - - +
176B GLU* 3.1 24.4 + - - +
217B SER* 4.8 19.1 - - - +
235B LEU* 3.9 29.4 - - + -
238B TYR* 3.5 48.2 - - + +
7G PDI 3.9 15.3 - - + -
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Residues in contact with TYR 173 (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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2B GLU* 2.9 36.9 + - + +
4B PRO* 3.4 16.3 - - + +
5B GLU* 2.4 45.5 + - - -
169B LEU* 4.0 5.2 - - + -
172B ILE* 1.3 82.2 - - + +
174B VAL* 1.3 59.6 + - - +
175B ASP 3.3 0.2 - - - -
176B GLU* 3.7 8.7 - - + +
177B VAL* 2.9 35.2 + - - +
207B ILE* 3.8 19.3 - - + -
208B LEU* 3.7 21.3 - - + -
211B ALA* 3.7 26.0 - - + +
217B SER* 2.7 20.4 + - - -
231B MSE 3.9 16.6 - - + -
235B LEU* 4.8 0.7 - - + -
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Residues in contact with VAL 174 (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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157B LYS* 3.3 39.3 - - + +
160B LEU* 3.6 40.4 - - + -
161B LEU* 4.1 14.6 - - + -
169B LEU* 4.1 11.9 - - + +
170B GLY 3.0 17.3 + - - +
171B ASN 4.1 2.0 - - - +
173B TYR* 1.3 75.0 - - - +
175B ASP* 1.3 74.1 + - - +
177B VAL* 3.7 3.1 - - - +
178B LEU* 2.8 37.8 + - + +
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Residues in contact with ASP 175 (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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157B LYS* 2.4 41.0 + - - +
171B ASN 3.5 7.7 + - - +
172B ILE 3.2 9.7 + - - +
174B VAL* 1.3 84.0 - - - +
176B GLU* 1.3 61.1 + - - +
178B LEU* 4.1 4.7 - - - +
179B TRP* 3.2 17.0 + - - +
185B PRO* 5.5 0.2 - - - +
237B VAL* 3.4 19.7 - - + +
238B TYR* 4.5 6.4 - - + -
261B GLY 3.9 0.7 - - - +
262B THR* 4.1 1.7 - - - +
263B HIS* 2.5 56.7 + - + +
269B GLN* 4.8 0.9 + - - +
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Residues in contact with GLU 176 (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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172B ILE* 3.1 17.7 + - + +
173B TYR* 3.9 10.3 - - + +
174B VAL 3.2 0.2 - - - -
175B ASP* 1.3 73.2 - - - +
177B VAL* 1.3 66.0 + - - +
179B TRP* 3.3 6.5 + - - +
180B LEU* 2.9 23.7 + - - +
207B ILE* 3.4 21.6 - - + +
231B MSE 5.1 2.4 - - + +
234B GLU 4.1 2.9 - - - +
235B LEU* 3.3 27.6 - - + +
236B GLN* 2.7 31.3 + - - +
237B VAL* 3.1 10.9 + - - +
238B TYR* 2.9 35.7 + - - +
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Residues in contact with VAL 177 (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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160B LEU* 5.0 4.0 - - + -
169B LEU* 4.1 13.0 - - + -
173B TYR 2.9 26.9 + - - +
174B VAL* 3.7 5.4 - - - +
176B GLU* 1.3 76.2 - - - +
178B LEU* 1.3 60.4 + - + +
180B LEU* 3.0 6.1 + - - +
181B ALA* 2.9 27.9 + - - +
200B LEU* 3.5 27.8 - - + -
203B SER* 4.0 11.1 - - - +
204B ILE* 3.8 37.2 - - + +
207B ILE* 3.6 17.9 - - + +
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Residues in contact with LEU 178 (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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156B ILE* 3.8 16.8 - - + -
157B LYS* 3.6 37.0 - - + -
160B LEU* 3.8 23.3 - - + -
174B VAL* 2.8 29.3 + - + +
175B ASP* 4.2 4.0 - - - +
177B VAL* 1.3 72.1 - - - +
179B TRP* 1.3 58.2 + - - +
181B ALA* 3.6 2.2 + - - -
182B LYS 3.2 1.9 + - - -
183B ILE* 2.8 49.8 + - + +
185B PRO* 3.6 20.4 - - + -
200B LEU* 3.9 13.0 - - + -
269B GLN* 3.8 6.3 - - - +
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Residues in contact with TRP 179 (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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175B ASP 3.2 18.6 + - - +
176B GLU* 3.6 5.4 - - - +
177B VAL 3.1 0.4 - - - -
178B LEU* 1.3 72.3 - - - +
180B LEU* 1.3 89.6 + - + +
181B ALA 3.0 4.0 - - - -
182B LYS* 2.8 20.6 + - - -
236B GLN* 3.2 52.3 - - + -
237B VAL* 3.4 24.9 - - + +
245B CYS* 3.5 19.6 - - - -
246B SER* 3.9 13.5 - - - -
247B ARG* 3.1 64.2 + - + +
252B ILE* 4.8 0.2 - - - +
265B CYS* 4.1 7.4 - - + +
269B GLN* 3.2 32.0 - - + +
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Residues in contact with LEU 180 (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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176B GLU 2.9 16.8 + - - +
177B VAL 3.0 5.4 + - - +
179B TRP* 1.3 98.0 - - + +
181B ALA* 1.3 57.9 + - - +
182B LYS* 3.4 2.2 + - - +
199B LEU* 4.2 9.2 - - + +
203B SER* 3.9 24.0 + - - +
206B GLU* 4.2 20.9 - - - +
207B ILE* 3.8 28.5 - - + -
247B ARG* 4.2 9.7 + - - +
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Residues in contact with ALA 181 (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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177B VAL 2.9 14.3 + - - +
178B LEU 4.3 1.3 - - - +
179B TRP 3.0 0.2 - - - -
180B LEU* 1.3 76.7 - - - +
182B LYS* 1.3 71.5 + - - +
183B ILE* 3.2 23.3 + - + +
196B SER* 5.5 1.9 + - - -
199B LEU* 3.6 24.3 - - + +
200B LEU* 4.0 22.0 - - + -
203B SER* 3.9 13.5 - - - +
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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