Contacts of the helix formed by residues 169 - 180 (chain A) in PDB entry 6J7Z
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 VAL 169 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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45A TRP* 3.8 34.1 - - + -
141A GLY 3.1 16.8 + - - +
142A ASN* 3.5 25.1 - - - +
167A ILE* 4.3 4.7 - - + +
168A ASP* 1.3 71.9 - - - +
170A SER* 1.3 57.1 + - - +
172A VAL* 3.2 9.7 + - - +
173A LYS* 2.9 24.6 + - - +
203A SER* 4.0 13.9 - - - +
206A GLU* 4.1 14.8 - - - +
207A LEU* 4.2 22.4 - - + +
210A TYR* 4.2 6.3 - - + -
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Residues in contact with SER 170 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142A ASN* 3.4 11.5 + - - +
143A SER* 3.0 22.9 + - - -
145A HIS* 5.1 0.7 - - - -
168A ASP* 3.1 16.6 + - - -
169A VAL* 1.3 79.2 - - - +
171A THR* 1.3 55.6 + - - +
173A LYS* 3.3 10.1 + - - +
174A GLU* 2.9 33.2 + - - +
165B ARG* 3.1 33.8 + - - -
166B ILE 4.7 2.7 - - - -
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Residues in contact with THR 171 (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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168A ASP* 3.1 29.3 + - - -
170A SER* 1.3 77.5 - - - +
172A VAL* 1.3 58.4 + - - +
174A GLU* 3.2 5.3 + - - +
175A LEU* 3.0 34.4 + - + +
166B ILE 3.3 11.4 + - - -
167B ILE* 4.2 7.3 - - + +
168B ASP* 2.9 50.1 + - - +
171B THR* 4.4 4.0 - - + -
172B VAL* 4.3 16.4 - - + -
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Residues in contact with VAL 172 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167A ILE* 6.2 0.2 - - + -
168A ASP 4.1 10.8 - - - +
169A VAL* 3.2 7.2 + - - +
171A THR* 1.3 77.2 - - + +
173A LYS* 1.3 57.4 + - - +
175A LEU* 3.7 7.6 - - + +
176A CYS* 2.9 28.6 + - - +
207A LEU* 4.2 9.0 - - + -
210A TYR* 3.5 35.2 - - + -
214A ILE* 4.2 6.1 - - + -
215A PHE* 4.0 19.3 - - + -
171B THR* 4.2 7.4 - - + -
172B VAL* 5.3 5.2 - - + -
175B LEU* 3.8 27.1 - - + -
215B PHE* 5.4 3.1 - - + -
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Residues in contact with LYS 173 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142A ASN* 5.2 2.5 - - - +
169A VAL 2.9 14.3 + - - +
170A SER* 3.4 13.0 - - - +
171A THR 3.2 0.2 - - - -
172A VAL* 1.3 76.8 - - - +
174A GLU* 1.3 63.2 + - - +
176A CYS* 3.3 2.4 + - - +
177A ARG* 2.9 28.1 + - + +
184A TYR* 3.2 29.1 + - + -
188A PRO 5.2 0.2 + - - -
189A LYS* 3.9 27.9 - - - +
206A GLU* 3.6 15.9 + - - +
210A TYR* 3.3 25.4 + - - +
165B ARG* 4.2 32.5 - - - +
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Residues in contact with GLU 174 (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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170A SER 2.9 19.3 + - - +
171A THR 3.2 4.2 + - - +
173A LYS* 1.3 81.3 - - + +
175A LEU* 1.3 59.6 + - - +
177A ARG* 3.0 31.0 + - - +
178A ARG* 2.4 69.4 + - - +
138B PRO* 5.2 3.6 - - + +
163B HIS* 5.5 2.1 - - - -
165B ARG* 3.5 37.9 + - + -
166B ILE 4.8 2.0 - - - +
167B ILE* 4.4 17.3 - - + -
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Residues in contact with LEU 175 (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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171A THR* 3.0 26.6 + - + +
172A VAL* 3.8 8.1 - - - +
174A GLU* 1.3 76.3 - - - +
176A CYS* 1.3 57.6 + - - +
178A ARG* 4.5 2.7 - - - +
179A TRP* 2.9 78.1 + - + +
180A TYR* 4.5 0.4 - - - -
214A ILE* 5.2 0.9 - - - -
43B MET* 4.7 4.7 - - + -
167B ILE* 4.1 27.6 - - + -
172B VAL* 3.8 28.9 - - + -
207B LEU* 4.2 11.4 - - + -
215B PHE* 4.2 13.9 - - + -
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Residues in contact with CYS 176 (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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172A VAL 2.9 18.5 + - - +
173A LYS 3.7 3.8 - - - +
175A LEU* 1.3 74.2 - - - +
177A ARG* 1.3 59.9 + - - +
180A TYR* 2.8 44.3 + - - +
183A GLU 4.4 2.0 - - - -
184A TYR* 3.7 25.4 - - + -
209A PHE* 5.2 0.9 - - - -
210A TYR* 3.7 25.6 - - + -
214A ILE* 3.7 36.9 - - + +
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Residues in contact with ARG 177 (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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173A LYS* 2.9 16.7 + - - +
174A GLU* 3.0 39.4 + - - +
176A CYS* 1.3 76.1 - - - +
178A ARG* 1.3 84.3 + - - +
181A PRO* 3.9 17.2 - - - +
184A TYR* 3.6 46.1 - - + -
40B ALA 4.8 4.0 + - - -
41B GLN* 3.6 35.0 + - - +
136B LEU 6.0 0.2 + - - -
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Residues in contact with ARG 178 (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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174A GLU* 2.4 54.0 + - - +
175A LEU* 4.0 3.4 - - - +
177A ARG* 1.3 92.5 - - - +
179A TRP* 1.3 75.2 + - + +
181A PRO* 4.2 5.9 - - - +
40B ALA 4.0 2.8 + - - -
41B GLN* 3.2 64.0 + - - +
42B ARG 3.7 1.4 + - - -
43B MET* 3.6 25.9 - - - +
70B SER* 3.8 9.3 + - - -
71B ASP* 5.6 0.5 - - - +
136B LEU 5.2 0.6 + - - -
138B PRO* 3.5 28.5 - - - +
167B ILE* 4.0 13.5 - - - +
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Residues in contact with TRP 179 (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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175A LEU* 2.9 61.1 + - + +
178A ARG* 1.3 84.9 - - + +
180A TYR* 1.3 71.7 + + + +
181A PRO* 3.6 2.4 - - - +
43B MET* 4.9 1.0 - - + +
70B SER* 2.8 25.7 + - - -
71B ASP* 4.1 3.6 - - - -
72B LEU* 4.1 23.1 - - + -
207B LEU* 4.1 17.5 - - + -
211B ARG* 3.4 73.8 + - + +
215B PHE* 4.2 24.0 - + - -
218B LYS* 2.8 29.6 + - - +
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Residues in contact with TYR 180 (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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175A LEU 4.5 3.4 - - - -
176A CYS* 2.8 15.9 + - - +
179A TRP* 1.3 97.4 - + + +
181A PRO* 1.3 61.2 - - - +
182A GLU 3.4 2.5 - - - -
183A GLU* 3.3 26.4 + - - +
184A TYR* 2.7 23.2 + - - +
214A ILE* 3.7 39.3 - - + -
211B ARG* 5.4 6.3 + - - +
215B PHE* 3.4 28.1 - + - +
216B LYS* 2.5 52.5 + - + -
218B LYS* 3.6 27.9 - - + +
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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