Contacts of the helix formed by residues 178 - 194 (chain A) in PDB entry 3RKQ
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 178 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172A ALA* 3.6 4.5 - - - +
177A LEU* 1.3 77.4 - - - +
179A SER* 1.3 64.3 + - - +
180A THR* 3.4 10.0 + - - -
181A GLN* 3.0 37.2 + - - +
182A VAL* 3.3 16.5 + - - +
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Residues in contact with SER 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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165A ALA* 5.9 0.2 - - - -
168A ARG* 3.8 20.4 + - - +
169A ASP* 2.5 30.8 + - - -
172A ALA* 3.7 15.2 - - - +
178A THR* 1.3 75.3 - - - +
180A THR* 1.3 57.6 + - - +
182A VAL* 3.4 2.1 + - - +
183A LYS* 2.9 29.3 + - - +
11D C 5.6 1.4 + - - -
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Residues in contact with THR 180 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178A THR* 3.2 9.6 + - - -
179A SER* 1.3 77.2 - - - +
181A GLN* 1.3 58.6 + - + +
183A LYS* 3.2 23.6 + - - +
184A ILE* 2.7 56.0 + - + +
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Residues in contact with GLN 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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143A VAL* 5.6 2.0 + - - +
145A PHE* 4.1 22.0 - - + -
177A LEU* 3.3 23.0 - - + +
178A THR* 3.0 40.6 + - - +
180A THR* 1.3 78.8 - - + +
182A VAL* 1.3 58.0 + - - +
184A ILE* 3.7 3.0 - - - +
185A TRP* 2.9 29.5 + - - +
4C A 2.6 42.4 + - - +
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Residues in contact with VAL 182 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153A LEU* 4.7 9.6 - - + -
163A LEU* 4.5 1.6 - - + -
168A ARG* 4.0 26.2 - - + +
171A LEU* 4.2 20.2 - - + -
172A ALA* 3.7 25.6 - - - +
175A LEU* 5.0 1.6 - - + -
177A LEU* 4.5 13.5 - - + -
178A THR 3.3 12.6 + - - +
179A SER 3.7 6.7 - - - +
180A THR 3.2 0.4 - - - -
181A GLN* 1.3 76.0 - - - +
183A LYS* 1.3 66.5 + - - +
185A TRP* 3.0 7.3 + - - +
186A PHE* 3.0 40.3 + - + -
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Residues in contact with LYS 183 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168A ARG* 3.8 24.9 - - - +
179A SER 2.9 16.8 + - - +
180A THR* 3.4 27.8 + - - +
182A VAL* 1.3 78.1 - - - +
184A ILE* 1.3 69.9 + - + +
186A PHE* 3.5 4.1 + - - +
187A GLN* 3.1 30.5 + - - +
190A ARG* 5.4 0.3 + - - -
10D C 5.0 1.2 - - - +
11D C 2.8 43.7 + - + +
12D C 3.6 25.5 + - + +
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Residues in contact with ILE 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 THR* 2.7 40.9 + - + +
181A GLN* 3.8 6.5 - - - +
183A LYS* 1.3 86.9 - - + +
185A TRP* 1.3 59.4 + - - +
187A GLN* 3.5 23.8 - - - +
188A ASN* 3.0 44.7 + - - +
3C A 4.9 1.3 - - + -
4C A 3.7 35.0 - - + +
5C G 5.8 2.9 - - - +
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Residues in contact with TRP 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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145A PHE* 3.8 23.5 - + + -
150A VAL* 4.7 10.6 - - + +
153A LEU* 3.6 59.3 - - + +
154A GLU* 3.8 21.1 - - + -
157A PHE* 4.1 6.5 - + + -
181A GLN 2.9 18.1 + - - +
182A VAL* 3.0 7.8 + - - +
184A ILE* 1.3 75.0 - - - +
186A PHE* 1.3 77.5 + + - +
188A ASN* 3.4 5.9 + - + +
189A ARG* 2.8 74.2 + - + +
192A LYS* 5.8 2.2 - - - +
3C A 3.4 29.9 + - - -
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Residues in contact with PHE 186 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153A LEU* 4.0 8.7 - - + -
156A ARG* 4.1 21.1 - - + -
157A PHE* 3.9 18.2 - + - -
160A GLN 3.4 22.0 - - - -
161A ARG 3.7 18.8 - - - -
162A TYR* 4.6 0.7 - - - -
163A LEU* 3.8 32.1 - - + +
168A ARG* 5.9 3.6 - - - -
171A LEU* 3.9 20.2 - - + -
182A VAL* 3.0 26.4 + - + +
183A LYS* 3.9 5.6 - - - +
185A TRP* 1.3 93.1 - + - +
187A GLN* 1.3 65.0 + - - +
189A ARG* 3.8 2.1 - - - +
190A ARG* 3.0 43.0 + - - +
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Residues in contact with GLN 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 LYS* 3.1 21.7 + - - +
184A ILE* 3.5 27.9 - - - +
186A PHE* 1.3 79.3 - - - +
188A ASN* 1.3 68.0 + - - +
190A ARG* 3.3 16.4 + - - +
191A TYR* 3.1 21.4 + - + +
5C G 4.6 4.9 + - - -
6C T 4.5 4.4 + - - -
12D C 4.1 22.3 + - + +
13D C 3.6 39.5 + - + +
14D A 3.6 24.4 - - - +
15D C 5.4 0.6 - - - +
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Residues in contact with ASN 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 ILE* 3.0 27.6 + - - +
185A TRP* 3.8 4.7 - - - +
187A GLN* 1.3 79.2 + - - +
189A ARG* 1.3 64.9 + - - +
191A TYR* 3.3 7.8 + - - +
192A LYS* 3.0 39.3 + - + +
3C A 3.6 25.2 + - - +
4C A 3.0 48.0 + - - +
5C G 4.5 1.6 - - - +
15D C 4.3 8.1 + - - -
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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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154A GLU* 2.9 30.7 + - - -
157A PHE* 3.6 43.2 - - + -
158A LYS* 6.4 0.4 - - - +
185A TRP* 2.8 51.3 + - + +
186A PHE 3.8 3.8 - - - +
187A GLN 3.3 0.2 - - - -
188A ASN* 1.3 73.2 - - - +
190A ARG* 1.3 57.5 + - - +
192A LYS* 3.3 20.1 + - - +
193A SER* 2.9 39.7 + - - +
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Residues in contact with ARG 190 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157A PHE* 4.1 4.9 - - + -
161A ARG* 2.5 59.6 + - - +
162A TYR* 3.2 53.1 - - - +
163A LEU 5.0 1.0 - - - +
183A LYS 5.4 0.4 + - - -
186A PHE* 3.0 43.3 + - - +
187A GLN* 3.6 12.6 - - - +
189A ARG* 1.3 76.0 - - - +
191A TYR* 1.3 65.8 + - - +
193A SER* 3.0 18.7 + - - -
194A LYS* 3.3 12.5 - - - +
12D C 4.2 14.1 + - - -
13D C 2.7 35.5 + - - +
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Residues in contact with TYR 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 GLN* 3.1 11.0 + - + +
188A ASN* 3.3 12.1 + - - +
190A ARG* 1.3 78.8 - - - +
192A LYS* 1.3 67.5 + - + +
194A LYS* 3.2 32.5 + - + +
13D C 4.9 2.2 - - + -
14D A 3.2 61.5 - + + +
15D C 3.5 56.0 + + - +
16D T 4.2 14.9 - - + +
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Residues in contact with LYS 192 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185A TRP* 5.8 2.2 - - - +
188A ASN* 3.0 32.3 + - + +
189A ARG* 3.7 18.7 - - - +
191A TYR* 1.3 81.5 - - + +
193A SER* 1.3 61.4 + - - +
194A LYS* 3.0 12.3 + - - +
2C G 4.1 31.3 + - + +
3C A 4.5 8.8 + - - -
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Residues in contact with SER 193 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157A PHE* 4.5 1.6 - - - -
161A ARG* 3.1 30.1 + - - -
189A ARG* 2.9 29.5 + - - +
190A ARG* 3.0 13.2 + - - -
192A LYS* 1.3 77.0 - - - +
194A LYS* 1.3 62.3 + - - +
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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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161A ARG* 4.4 13.2 - - - +
190A ARG 3.3 17.7 - - - +
191A TYR* 3.2 19.5 - - + +
192A LYS* 3.0 6.7 - - - +
193A SER* 1.3 85.4 - - - +
13D C 5.9 0.2 - - - -
14D A 3.6 28.2 + - - +
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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