Contacts of the helix formed by residues 175 - 188 (chain A) in PDB entry 3L2P
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 LEU 175 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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169A MET 5.9 0.2 - - - +
170A ARG* 4.9 5.8 - - - +
171A HIS 3.3 26.0 - - - +
172A LYS* 3.2 22.6 + - + +
173A ASP 3.4 1.5 - - - +
174A CYS* 1.3 81.3 - - + +
176A LEU* 1.3 67.2 + - - +
177A ARG* 3.9 20.6 - - + +
178A GLU* 2.9 19.0 + - + +
179A PHE* 2.9 10.9 + - - +
283A SER 4.7 12.8 - - - +
284A LEU* 5.5 5.2 - - + +
285A LEU 3.5 11.0 - - - +
286A THR* 5.6 5.8 - - + -
287A ILE* 4.5 2.0 - - - -
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Residues in contact with LEU 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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174A CYS 3.8 1.4 + - - -
175A LEU* 1.3 70.7 - - - +
177A ARG* 1.3 52.8 + - - +
179A PHE* 3.4 15.7 - - + +
180A ARG* 2.7 41.1 + - - +
283A SER* 4.2 3.1 - - - +
285A LEU* 3.0 26.9 + - + +
287A ILE* 4.2 7.7 - - + +
290A VAL* 3.9 29.8 - - + -
317A CYS* 5.9 0.2 - - - -
321A ASP* 3.3 50.9 - - + +
324A CYS* 3.8 26.0 - - - -
325A ILE* 4.3 9.0 - - + -
328A LEU* 5.5 1.1 - - + -
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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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175A LEU* 2.9 19.5 + - + +
176A LEU* 1.3 77.3 - - - +
178A GLU* 1.3 63.7 + - + +
180A ARG* 3.7 21.3 - - - +
181A LYS* 2.9 62.9 + - + +
283A SER* 3.9 26.2 + - - +
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Residues in contact with GLU 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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172A LYS* 3.2 33.1 - - + +
173A ASP* 4.6 5.4 - - - +
175A LEU* 2.9 11.7 + - + +
177A ARG* 1.3 84.6 + - + +
179A PHE* 1.3 65.7 + - - +
181A LYS* 3.0 34.1 + - - +
182A LEU* 2.8 23.4 + - - +
202A PHE* 4.4 25.9 - - + -
206A GLY 6.0 2.9 - - - +
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Residues in contact with PHE 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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173A ASP 5.6 0.8 + - - -
175A LEU 2.9 12.0 + - - +
176A LEU* 3.4 13.2 - - + +
178A GLU* 1.3 75.7 - - - +
180A ARG* 1.3 64.6 + - - +
182A LEU* 3.1 14.0 + - + +
183A CYS* 2.9 35.6 + - - -
202A PHE* 5.4 2.6 - - - -
219A THR* 3.9 21.8 - - + -
222A LEU* 3.5 45.5 - - + -
223A LEU* 3.8 25.4 - - + -
287A ILE* 4.0 23.1 - - + -
324A CYS* 4.1 24.7 - - - -
328A LEU* 4.3 7.6 - - + -
333A LEU* 4.1 6.1 - - + -
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Residues in contact with ARG 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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176A LEU* 2.7 25.4 + - - +
177A ARG* 3.7 15.8 - - - +
179A PHE* 1.3 72.1 - - - +
181A LYS* 1.3 58.2 + - - +
183A CYS* 2.8 8.5 + - + +
184A ALA* 2.6 41.8 + - + +
283A SER* 4.0 6.7 + - - -
318A THR* 3.4 15.0 - - - +
320A ASN* 3.0 44.1 + - - +
321A ASP* 3.1 29.7 + - - +
323A LYS* 6.5 0.7 - - - -
324A CYS* 4.6 14.1 - - + +
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Residues in contact with LYS 181 (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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177A ARG* 2.9 58.2 + - + +
178A GLU* 3.1 33.7 - - - +
180A ARG* 1.3 75.2 - - - +
182A LEU* 1.3 57.1 + - - +
184A ALA* 3.2 6.1 + - - +
185A MET* 2.9 43.6 + - + +
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Residues in contact with LEU 182 (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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178A GLU 2.8 10.1 + - - +
179A PHE* 3.2 17.3 - - + +
181A LYS* 1.3 77.3 - - - +
183A CYS* 1.3 63.9 + - - +
185A MET* 3.3 5.1 + - - +
186A VAL* 3.2 25.3 + - + +
198A ILE* 4.3 11.0 - - + -
199A ILE* 3.8 37.0 - - + -
202A PHE* 3.7 46.0 - - + -
203A LEU* 5.4 0.4 - - + -
219A THR* 5.3 6.7 - - + -
223A LEU* 4.4 24.0 - - + -
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Residues in contact with CYS 183 (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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179A PHE* 2.9 44.6 + - - +
180A ARG* 2.8 11.7 + - + +
182A LEU* 1.3 74.5 - - - +
184A ALA* 1.3 67.1 + - - +
186A VAL* 3.6 0.4 + - - -
187A ALA* 3.2 24.9 + - - +
223A LEU* 4.1 7.6 - - - -
324A CYS* 5.7 2.5 - - - -
333A LEU* 3.7 12.6 - - + +
335A MET* 3.3 33.6 - - + +
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Residues in contact with ALA 184 (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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180A ARG* 2.6 26.7 + - + +
181A LYS* 3.6 6.5 - - - +
183A CYS* 1.3 72.8 - - - +
185A MET* 1.3 63.0 + - + +
187A ALA* 3.6 2.4 + - - -
188A ASP* 2.9 40.4 + - - +
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Residues in contact with MET 185 (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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181A LYS* 2.9 29.8 + - + +
182A LEU* 3.7 6.5 - - - +
183A CYS 3.2 0.2 - - - -
184A ALA* 1.3 78.1 - - + +
186A VAL* 1.3 63.7 + - - +
188A ASP* 3.0 15.8 + - - +
189A ASN* 3.4 16.3 + - - +
198A ILE* 4.0 32.1 - - + -
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Residues in contact with VAL 186 (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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182A LEU* 3.2 20.1 + - + +
183A CYS 4.1 3.1 - - - +
185A MET* 1.3 74.8 - - - +
187A ALA* 1.3 61.8 + - - +
189A ASN* 3.3 11.3 + - - +
195A LYS* 3.2 51.0 + - + +
198A ILE* 4.2 8.1 - - + -
199A ILE* 3.2 32.5 - - + -
223A LEU* 6.3 0.4 - - + -
335A MET* 4.0 16.4 - - + -
337A SER* 4.0 22.2 - - - -
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Residues in contact with ALA 187 (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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183A CYS 3.2 19.0 + - - +
184A ALA* 3.9 2.0 - - - +
186A VAL* 1.3 71.7 - - - +
188A ASP* 1.3 67.6 + - - +
189A ASN 3.0 10.1 + - - -
190A PRO* 5.0 0.9 - - - +
195A LYS* 4.5 4.7 + - - -
333A LEU 5.5 0.2 - - - +
334A LYS 3.8 8.3 - - - +
335A MET* 3.8 30.5 - - + +
336A ASN* 5.3 4.4 + - - +
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Residues in contact with ASP 188 (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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184A ALA* 2.9 26.6 - - - +
185A MET* 3.0 8.1 + - - +
187A ALA* 1.3 84.0 - - - +
189A ASN* 1.3 62.3 + - - +
190A PRO* 3.8 8.7 - - - +
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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