Contacts of the helix formed by residues 170 - 183 (chain A) in PDB entry 4RQI
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 GLU 170 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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116A LEU* 4.2 11.7 - - + -
165A CYS* 2.7 24.3 + - + +
168A ASN* 3.7 23.5 - - + +
169A LYS* 1.3 72.1 - - - +
171A PHE* 1.3 58.2 + - - +
172A GLU 3.4 2.9 - - - -
173A LYS* 3.4 24.5 + - + +
174A ALA* 3.0 25.8 + - - +
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Residues in contact with PHE 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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166A ILE* 4.2 26.0 - - + -
169A LYS* 3.3 52.4 + - + -
170A GLU* 1.3 70.1 - - - +
172A GLU* 1.3 60.8 + - - +
174A ALA* 3.5 5.9 - - - +
175A SER* 2.9 30.1 + - - -
198A ILE 4.9 0.2 - - - -
199A ILE* 3.9 36.7 - - + +
202A LYS* 3.5 59.0 - - + +
204A LEU* 4.3 9.6 - - + -
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Residues in contact with GLU 172 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170A GLU 3.4 0.6 - - - -
171A PHE* 1.3 76.7 - - - +
173A LYS* 1.3 64.9 + - - +
175A SER* 3.2 8.4 + - - -
176A LYS* 3.0 23.1 + - + +
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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
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116A LEU* 4.6 13.8 + - + -
125A GLU 4.9 5.7 + - - -
127A THR* 3.6 29.0 - - + +
130A GLU* 4.9 2.9 + - - +
165A CYS* 3.3 25.1 - - + -
170A GLU* 3.4 28.3 + - + +
171A PHE 3.3 0.4 - - - -
172A GLU* 1.3 81.4 - - - +
174A ALA* 1.3 61.1 + - - +
176A LYS* 3.4 20.5 + - + +
177A ILE* 3.0 39.2 + - + +
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Residues in contact with ALA 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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162A VAL* 4.1 10.4 - - + +
165A CYS* 3.9 15.0 - - + +
166A ILE* 3.9 20.9 - - + -
170A GLU 3.0 14.1 + - - +
171A PHE* 3.5 10.5 - - - +
172A GLU 3.2 0.2 - - - -
173A LYS* 1.3 77.5 - - - +
175A SER* 1.3 56.4 + - - +
177A ILE* 3.6 3.6 + - - +
178A LEU* 2.9 31.0 + - - +
199A ILE* 3.7 18.8 - - + -
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Residues in contact with SER 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 PHE 2.9 16.5 + - - -
172A GLU* 3.5 7.6 - - - -
174A ALA* 1.3 76.5 - - - +
176A LYS* 1.3 53.2 + - - +
178A LEU* 3.3 7.5 + - - +
179A LYS* 2.8 36.5 + - - +
196A LEU* 4.8 11.1 - - - +
199A ILE* 4.0 18.1 - - - +
200A ARG* 5.9 0.9 + - - -
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Residues in contact with LYS 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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125A GLU* 3.1 33.0 + - - -
126A LEU* 4.5 1.5 - - - +
130A GLU* 3.2 29.2 + - - +
172A GLU* 3.0 15.0 + - + +
173A LYS* 3.6 24.0 - - + +
175A SER* 1.3 72.3 - - - +
177A ILE* 1.3 61.2 + - + +
179A LYS* 3.1 8.8 + - - +
180A LYS* 2.8 44.2 + - + +
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Residues in contact with ILE 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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127A THR* 4.2 4.0 - - - +
130A GLU* 3.4 40.8 - - + +
133A ILE* 5.4 1.3 - - + -
158A LYS* 4.9 1.6 - - - +
161A ALA* 4.1 20.9 - - + +
162A VAL* 3.7 18.6 - - + -
165A CYS* 3.7 29.4 - - - -
173A LYS* 3.0 18.7 + - + +
174A ALA* 3.9 3.8 - - - +
176A LYS* 1.3 79.3 - - + +
178A LEU* 1.3 62.8 + - - +
180A LYS* 3.3 1.1 + - - -
181A HIS* 3.0 46.5 + - + +
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Residues in contact with LEU 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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162A VAL* 4.1 10.5 - - + +
174A ALA 2.9 18.4 + - - +
175A SER* 3.4 5.6 - - - +
177A ILE* 1.3 77.3 - - - +
179A LYS* 1.3 62.3 + - - +
182A MET* 3.0 60.5 + - - +
183A SER 3.6 2.1 + - - -
192A ARG* 4.0 14.2 - - + +
195A LEU* 3.9 19.7 - - + -
196A LEU* 3.6 50.7 - - + +
199A ILE* 4.0 14.1 - - + -
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Residues in contact with LYS 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 SER 2.8 20.7 + - - +
176A LYS* 3.5 7.2 - - - +
178A LEU* 1.3 73.4 - - - +
180A LYS* 1.3 61.7 + - + +
183A SER* 3.1 34.7 - - - -
184A LYS* 5.1 11.3 + - - +
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Residues in contact with LYS 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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125A GLU* 4.8 4.9 + - - -
126A LEU* 4.5 22.6 - - - +
130A GLU* 5.2 2.1 + - - +
134A ASN* 6.1 2.6 - - - +
176A LYS* 2.8 32.5 + - + +
177A ILE* 5.8 0.2 - - - -
179A LYS* 1.3 77.6 - - + +
181A HIS* 1.3 91.4 + - + +
182A MET 3.8 0.2 - - - -
183A SER 5.1 0.2 - - - -
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Residues in contact with HIS 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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126A LEU* 6.4 0.2 - - - +
130A GLU* 4.7 15.1 + - + +
133A ILE* 3.9 41.3 - - + +
134A ASN* 5.2 6.7 - - - -
158A LYS* 2.9 52.9 + - + +
177A ILE* 3.0 41.6 + - + +
180A LYS* 1.3 112.2 + - + +
182A MET* 1.3 63.1 + - + +
184A LYS 5.2 0.7 - - - -
185A ASP* 4.1 2.8 - - - +
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Residues in contact with MET 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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155A LYS 4.6 0.9 - - - +
158A LYS* 3.6 31.4 - - + +
159A GLU* 3.7 19.3 - - + +
162A VAL* 4.9 2.2 - - + -
178A LEU* 3.0 37.3 + - + +
180A LYS 3.8 0.4 - - - -
181A HIS* 1.3 86.9 - - + +
183A SER* 1.3 67.6 + - - +
184A LYS 3.2 3.5 + - - +
185A ASP* 4.1 1.8 - - - -
188A THR* 3.5 32.2 + - + +
189A GLN* 3.2 17.7 + - - -
191A LEU* 4.1 15.0 - - + -
192A ARG* 3.8 34.9 - - + -
195A LEU* 4.2 6.5 - - + -
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Residues in contact with SER 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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178A LEU 3.6 3.4 + - - -
179A LYS* 3.1 31.6 + - - -
180A LYS 5.1 0.2 - - - -
182A MET* 1.3 80.3 - - - +
184A LYS* 1.3 72.8 + - - +
185A ASP 3.6 0.2 - - - -
189A GLN* 3.6 12.1 + - - +
192A ARG* 4.7 9.6 - - - +
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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