Contacts of the helix formed by residues 189 - 199 (chain A) in PDB entry 4RWN
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 PHE 189 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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87A PHE* 4.0 22.7 - + - -
154A ALA* 4.1 11.2 - - + -
155A LEU* 3.8 31.9 - - + -
168A ILE* 4.2 8.3 - - + -
169A TYR* 3.8 21.8 - + - -
172A LEU* 3.9 26.9 - - + -
185A PHE 3.5 20.6 - - - -
186A SER* 2.9 14.5 + - - +
188A CYS* 1.3 81.4 - - + +
190A THR* 1.3 57.1 + - - +
191A GLU 3.1 3.4 - - - -
192A LEU* 2.9 36.7 + - + +
193A GLN* 3.1 12.5 + - - +
302A ALA* 3.7 24.7 - - + +
303A ASP* 4.8 3.6 - - + -
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Residues in contact with THR 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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58A VAL* 3.7 23.8 - - + -
60A GLY* 3.7 12.7 - - - -
61A GLY 4.5 0.9 + - - -
78A VAL* 3.7 17.5 - - + -
80A PHE* 4.5 6.7 - - + -
186A SER 3.4 1.5 + - - -
187A THR 3.3 17.8 + - - +
188A CYS 3.5 1.2 + - - -
189A PHE* 1.3 77.2 - - - +
191A GLU* 1.3 55.7 + - + +
193A GLN* 3.2 14.7 + - - +
194A ARG* 2.8 35.0 + - - +
401A APC 5.1 0.3 + - - -
402A APC 3.0 32.5 + - - -
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Residues in contact with GLU 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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56A LYS* 3.0 37.8 + - - +
58A VAL* 3.9 29.4 - - + -
80A PHE* 4.6 6.1 - - - -
153A ASP* 4.8 0.2 - - - +
155A LEU* 4.1 19.6 - - + +
158A TRP* 4.1 32.8 + - + +
188A CYS 4.8 1.2 - - - +
189A PHE 3.1 0.2 - - - -
190A THR* 1.3 79.8 - - + +
192A LEU* 1.3 57.3 + - - +
194A ARG* 3.6 16.4 + - - +
195A ASP* 2.9 28.2 + - - +
3C C 4.6 2.9 + - - +
4C A 4.0 17.2 + - - +
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Residues in contact with LEU 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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155A LEU* 3.7 18.6 - - + -
158A TRP* 3.4 41.3 - - + +
164A PRO* 3.7 15.5 - - + -
169A TYR* 3.2 27.4 - - - +
189A PHE* 2.9 25.7 + - + +
191A GLU* 1.3 73.9 - - - +
193A GLN* 1.3 66.1 + - - +
195A ASP* 3.3 3.8 + - - -
196A PHE* 3.0 20.4 + - - +
275A TYR* 3.1 31.6 + - + -
302A ALA* 3.7 12.3 - - + +
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Residues in contact with GLN 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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65A LYS* 3.6 14.0 - - - -
186A SER* 3.8 12.6 - - - -
189A PHE 3.1 7.2 + - - +
190A THR* 3.4 8.6 + - - +
192A LEU* 1.3 77.5 - - - +
194A ARG* 1.3 62.4 + - - +
196A PHE* 3.3 18.5 + - - +
197A LEU* 3.8 4.5 + - - +
230A TYR* 3.8 16.2 + - - +
300A ASP* 2.7 27.7 + - - -
301A PRO* 5.9 0.7 - - - -
302A ALA* 3.5 18.6 - - + +
401A APC 2.7 51.5 + - - +
402A APC 3.2 24.0 + - - -
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Residues in contact with ARG 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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58A VAL* 4.1 13.1 - - + +
59A LYS* 3.0 28.9 + - - +
60A GLY* 4.8 6.5 - - - -
61A GLY 5.7 0.2 - - - +
64A GLY* 3.3 33.9 - - - +
65A LYS* 3.9 13.3 - - + +
190A THR 2.8 19.5 + - - +
191A GLU* 3.8 16.7 + - - +
193A GLN* 1.3 73.1 - - - +
195A ASP* 1.3 59.1 + - - +
197A LEU* 3.1 5.0 + - - +
198A ARG* 2.9 66.6 + - + +
4C A 4.2 16.2 + - - -
5C U 2.8 35.1 + - - -
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Residues in contact with ASP 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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158A TRP* 3.5 30.9 - - + -
160A PRO* 4.3 11.3 - - - +
161A GLY* 4.6 7.1 + - - -
191A GLU 2.9 19.5 + - - +
192A LEU 3.3 1.8 + - - +
194A ARG* 1.3 77.1 - - - +
196A PHE* 1.3 60.1 + - - +
197A LEU 3.1 1.4 + - - -
198A ARG* 3.8 20.8 + - - +
199A ASN* 4.5 12.7 + - - +
275A TYR* 2.9 24.2 + - - +
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Residues in contact with PHE 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 LEU 3.0 12.3 + - - +
193A GLN* 3.5 13.2 - - - +
194A ARG 3.1 0.4 - - - -
195A ASP* 1.3 77.0 - - - +
197A LEU* 1.3 68.5 + - + +
199A ASN* 5.5 0.2 - - - -
200A ARG* 2.7 55.7 + - - +
230A TYR* 5.5 0.7 - - - +
234A LEU* 3.8 15.3 - - + -
237A VAL* 3.9 13.7 - - + -
241A GLU* 5.1 0.2 - - - -
272A TRP* 3.4 42.0 - + - -
274A ALA* 4.2 11.2 - - + -
275A TYR* 3.2 15.7 + + + +
301A PRO* 3.7 35.9 - - + -
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Residues in contact with LEU 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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65A LYS* 3.9 34.3 - - + +
67A THR* 5.0 4.0 - - + -
193A GLN 3.9 10.1 - - - +
194A ARG 3.1 1.2 + - - -
196A PHE* 1.3 102.0 - - + +
198A ARG* 1.3 63.7 + - - +
199A ASN* 3.3 2.7 - - - -
200A ARG* 3.0 28.8 + - + +
205A LYS* 3.3 12.5 - - + -
208A ILE* 3.6 30.3 - - + -
230A TYR* 5.2 1.8 - - + +
233A GLU* 4.1 24.5 - - + +
234A LEU* 5.0 4.7 - - + -
237A VAL* 3.7 17.7 - - + -
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Residues in contact with ARG 198 (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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59A LYS* 6.2 1.2 - - - +
64A GLY* 4.0 17.9 + - - +
65A LYS 3.9 6.3 - - - +
160A PRO* 5.8 6.1 - - - +
194A ARG* 2.9 65.2 + - - +
195A ASP* 3.8 15.5 + - - +
197A LEU* 1.3 75.2 - - - +
199A ASN* 1.3 60.0 + - + +
205A LYS* 2.7 25.6 + - - +
7B U 4.5 0.2 + - - -
8B G 3.2 33.3 - - - +
9B A 3.7 23.5 + - - -
4C A 5.2 4.4 + - - -
5C U 4.7 5.1 + - - -
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Residues in contact with ASN 199 (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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195A ASP* 4.5 12.7 + - - +
198A ARG* 1.3 76.8 - - + +
200A ARG* 1.3 79.5 + - - +
201A PRO* 3.7 2.1 - - - +
8B G 3.8 25.5 + - - +
9B A 4.6 12.9 - - - +
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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