Contacts of the helix formed by residues 177 - 197 (chain A) in PDB entry 4RDU
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 THR 177 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139A LYS* 4.6 3.0 + - - +
171A ALA* 3.7 1.8 - - - -
176A LEU* 1.3 76.0 - - - +
178A GLN* 1.3 58.9 + - - +
179A THR* 3.3 11.4 + - - -
180A GLN* 2.9 41.1 + - - +
181A VAL* 3.0 27.4 + - - +
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Residues in contact with GLN 178 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164A LEU* 4.1 3.6 - - - +
167A ARG* 2.9 47.5 + - - +
168A ALA* 3.6 39.7 + - - +
171A ALA* 3.7 13.2 - - + +
177A THR* 1.3 72.8 - - - +
179A THR* 1.4 57.1 + - - +
181A VAL* 3.4 3.7 + - - +
182A LYS* 2.8 31.3 + - - +
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Residues in contact with THR 179 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139A LYS* 4.2 15.7 - - - +
177A THR* 3.2 10.1 + - - -
178A GLN* 1.4 74.9 - - - +
180A GLN* 1.3 65.9 + - - +
182A LYS* 3.7 19.2 + - - +
183A ILE* 2.9 38.2 + - + +
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Residues in contact with GLN 180 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139A LYS* 3.9 20.7 - - - +
142A THR* 2.7 40.9 + - - +
144A TYR* 3.3 22.6 + - - +
175A GLY 4.8 0.5 - - - +
176A LEU* 3.5 22.6 - - + +
177A THR* 2.9 47.9 + - - +
179A THR* 1.3 75.4 - - - +
181A VAL* 1.3 63.9 + - - +
183A ILE* 3.9 1.6 - - - +
184A TRP* 3.0 18.9 + - - +
7C A 4.5 8.1 - - - +
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Residues in contact with VAL 181 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144A TYR* 5.2 0.2 - - - -
152A LEU* 4.5 8.5 - - + -
162A LEU* 3.8 28.5 - - + -
167A ARG* 4.1 8.5 - - + +
170A LEU* 3.9 13.0 - - + +
171A ALA* 3.6 36.3 - - + +
174A LEU* 5.4 0.2 - - + -
176A LEU* 4.0 19.1 - - + -
177A THR 3.0 10.3 + - - +
178A GLN* 3.4 6.7 + - - +
180A GLN* 1.3 77.9 - - - +
182A LYS* 1.3 62.0 + - - +
184A TRP* 3.2 6.3 + - - +
185A PHE* 3.0 31.7 + - + -
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Residues in contact with LYS 182 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162A LEU* 6.2 0.9 - - - -
167A ARG* 3.8 30.2 - - - +
178A GLN 2.8 20.7 + - - +
179A THR* 3.4 20.2 + - - +
181A VAL* 1.3 72.8 - - - +
183A ILE* 1.3 75.7 + - - +
185A PHE* 3.5 6.0 + - - +
186A GLN* 3.0 43.4 + - - +
189A ARG* 5.0 0.3 + - - -
3B A 3.5 25.6 + - - +
4B C 3.6 21.0 + - + +
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Residues in contact with ILE 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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139A LYS* 6.2 0.7 - - - +
179A THR* 2.9 31.1 + - + +
180A GLN 3.9 3.1 - - - +
182A LYS* 1.3 83.1 - - - +
184A TRP* 1.3 59.9 + - - +
186A GLN* 3.3 31.8 + - - +
187A ASN* 2.8 48.6 + - - +
6C A 4.4 1.8 - - + -
7C A 3.6 39.7 - - + +
8C T 3.8 17.5 - - + -
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Residues in contact with TRP 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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144A TYR* 4.0 19.3 - + - +
149A LEU* 4.0 14.4 - - + +
152A LEU* 3.7 56.7 - - + +
153A GLN* 3.6 38.3 - - + +
156A PHE* 4.0 11.7 - + + -
180A GLN 3.0 18.2 + - - +
181A VAL* 3.6 7.2 - - - +
183A ILE* 1.3 76.7 - - - +
185A PHE* 1.3 72.3 + + - +
187A ASN* 3.2 2.9 + - - +
188A LYS* 2.7 66.7 + - + +
6C A 3.3 31.5 + - - -
7C A 5.7 0.2 + - - -
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Residues in contact with PHE 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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152A LEU* 4.0 8.5 - - + -
155A ARG* 4.3 9.9 - - + -
156A PHE* 3.6 19.1 - + - -
159A THR 3.2 26.2 - - - -
160A GLN 3.6 18.8 - - - -
162A LEU* 3.7 42.2 - - + -
170A LEU* 3.8 17.7 - - + -
181A VAL* 3.0 26.2 + - + +
182A LYS* 3.8 5.6 - - - +
184A TRP* 1.3 94.9 - + - +
186A GLN* 1.3 62.7 + - - +
188A LYS* 3.9 1.6 - - - +
189A ARG* 3.0 44.1 + - - +
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Residues in contact with GLN 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 LYS* 3.0 36.9 + - + +
183A ILE* 3.3 33.9 - - - +
185A PHE* 1.3 73.6 - - - +
187A ASN* 1.3 63.0 + - - +
189A ARG* 3.8 18.5 - - - +
190A SER* 3.0 28.2 + - - -
4B C 4.5 13.5 + - - +
5B T 3.4 43.8 + - + +
6B A 4.7 2.5 + - - +
8C T 4.3 13.3 - - - +
9C T 4.8 1.2 - - - +
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Residues in contact with ASN 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 ILE* 2.8 32.1 + - - +
184A TRP 3.8 2.9 - - - +
186A GLN* 1.3 77.4 - - - +
188A LYS* 1.3 57.6 + - - +
190A SER* 3.2 9.4 + - - -
191A LYS* 2.9 27.7 + - - +
7B A 4.9 1.9 + - - -
5C T 5.0 5.4 - - + -
6C A 3.2 37.3 + - - +
7C A 3.0 45.8 + - - +
8C T 4.8 1.7 - - - +
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Residues in contact with LYS 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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153A GLN* 3.0 34.8 + - - +
156A PHE* 3.7 36.1 - - + -
184A TRP* 2.7 49.3 + - + +
185A PHE 3.9 3.4 - - - +
187A ASN* 1.3 75.1 - - - +
189A ARG* 1.4 60.3 + - - +
191A LYS* 3.2 37.8 + - + +
192A ILE* 3.2 29.5 + - - +
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Residues in contact with ARG 189 (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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156A PHE* 3.7 21.5 - - + -
160A GLN* 2.8 37.9 + - + +
161A TYR* 3.3 40.2 - - - +
162A LEU 5.0 0.6 - - - +
185A PHE* 3.0 38.5 + - - +
186A GLN* 3.8 21.0 - - - +
188A LYS* 1.4 74.6 - - - +
190A SER* 1.3 58.2 + - - +
192A ILE* 3.4 6.2 + - - +
193A LYS* 3.0 28.6 + - - +
4B C 3.5 30.1 + - - -
5B T 3.0 37.2 + - - +
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Residues in contact with SER 190 (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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186A GLN 3.0 17.6 + - - -
187A ASN* 3.2 11.4 + - - -
189A ARG* 1.3 74.3 - - - +
191A LYS* 1.3 64.6 + - - +
193A LYS* 3.3 6.6 + - - +
194A LYS* 3.0 48.4 + - - +
6B A 4.5 22.4 + - - -
7B A 5.3 3.5 + - - -
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Residues in contact with LYS 191 (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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187A ASN 2.9 13.4 + - - +
188A LYS* 3.2 39.0 + - + +
190A SER* 1.3 78.1 - - - +
192A ILE* 1.3 66.4 + - + +
194A LYS* 3.4 6.8 + - - +
195A ILE* 3.1 41.5 + - + +
4C C 4.2 17.4 + - - -
5C T 2.5 36.0 + - + +
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Residues in contact with ILE 192 (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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156A PHE* 4.1 19.7 - - + -
160A GLN* 5.3 10.1 - - - +
188A LYS* 3.2 33.1 + - - +
189A ARG* 3.6 7.4 - - - +
190A SER 3.3 0.2 - - - -
191A LYS* 1.3 88.0 - - + +
193A LYS* 1.3 65.7 + - - +
195A ILE* 3.3 15.1 + - + +
196A MET* 2.9 38.1 + - + +
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Residues in contact with LYS 193 (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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189A ARG 3.0 16.5 + - - +
190A SER* 3.3 8.0 + - - +
192A ILE* 1.3 77.3 - - - +
194A LYS* 1.3 64.2 + - + +
196A MET* 3.2 30.6 + - + +
197A LYS* 3.1 37.4 + - + +
5B T 5.4 0.2 - - - +
6B A 3.4 30.1 - - - +
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Residues in contact with LYS 194 (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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190A SER* 3.0 37.2 + - - +
191A LYS* 3.8 5.8 - - - +
192A ILE 3.3 0.2 - - - -
193A LYS* 1.3 75.3 - - + +
195A ILE* 1.3 64.9 + - - +
197A LYS* 3.3 6.4 + - - +
198A ASN* 3.0 23.8 + - - +
6B A 5.1 3.4 - - - +
7B A 4.7 20.1 + - - -
8B T 4.1 26.5 - - - +
5C T 5.9 9.0 - - + -
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Residues in contact with ILE 195 (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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191A LYS* 3.1 43.9 + - + +
192A ILE* 3.3 16.8 + - + +
194A LYS* 1.3 75.2 - - - +
196A MET* 1.3 65.2 + - + +
198A ASN* 3.0 43.0 + - - +
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Residues in contact with MET 196 (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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192A ILE* 2.9 33.2 + - + +
193A LYS* 3.2 28.2 + - + +
195A ILE* 1.3 79.8 - - + +
197A LYS* 1.3 82.5 + - + +
198A ASN* 3.4 2.5 + - - +
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Residues in contact with LYS 197 (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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193A LYS* 3.1 29.7 + - + +
194A LYS* 3.5 6.7 - - - +
195A ILE 3.2 0.2 - - - -
196A MET* 1.3 101.3 - - - +
198A ASN* 1.3 66.7 + - - +
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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
------------------------------------------------------------
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