Contacts of the helix formed by residues 190 - 199 (chain A) in PDB entry 1I4W
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 SER 190 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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179A LYS* 4.4 12.8 - - - +
188A SER 3.2 10.1 + - - -
189A ARG* 1.3 77.9 + - - +
191A LYS* 1.3 67.3 + - - +
192A CYS* 3.2 17.0 - - - -
193A SER* 2.7 20.7 + - - -
194A VAL* 3.2 13.2 - - - +
267A MET* 3.7 10.5 - - - -
270A LYS* 3.6 12.3 + - - +
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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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148A MET* 3.6 28.5 - - + +
190A SER* 1.3 75.4 - - - +
192A CYS* 1.3 57.7 + - - +
194A VAL* 3.1 11.1 + - + +
195A VAL* 2.9 51.0 + - + +
259A TRP* 4.6 3.1 - - - -
260A ASP* 2.9 26.8 + - - -
263A THR* 3.2 37.9 + - - +
264A ARG* 3.9 20.2 - - - +
267A MET* 4.1 18.5 - - + +
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Residues in contact with CYS 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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144A GLU 5.9 1.6 - - - +
147A ILE* 5.6 3.6 - - + -
148A MET* 3.8 27.5 - - + -
151A LEU* 4.5 11.1 - - + +
176A THR 5.6 0.7 - - - -
179A LYS* 4.1 9.9 - - - -
180A LEU* 4.0 28.4 - - + +
190A SER* 3.2 16.9 - - - -
191A LYS* 1.3 78.1 - - - +
193A SER* 1.3 62.9 + - - +
195A VAL* 3.8 4.1 - - - +
196A ARG* 2.8 30.5 + - - +
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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
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179A LYS 2.8 21.5 + - - -
180A LEU 3.3 13.7 - - - -
182A ALA* 3.4 21.8 - - - -
189A ARG* 3.6 12.2 - - - -
190A SER* 2.7 29.8 + - - -
192A CYS* 1.3 78.8 - - - +
194A VAL* 1.3 52.9 + - - +
196A ARG* 3.3 5.9 + - - -
197A GLU* 2.7 35.9 + - - +
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Residues in contact with VAL 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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189A ARG* 4.2 13.0 - - - +
190A SER 3.2 16.6 - - - +
191A LYS* 3.1 10.5 + - + +
193A SER* 1.3 77.1 - - - +
195A VAL* 1.3 57.6 + - + +
197A GLU* 3.2 10.7 + - - +
198A ALA* 2.8 27.7 + - - +
259A TRP* 4.4 9.0 - - + -
263A THR* 4.6 5.6 - - + -
267A MET* 3.6 24.0 - - + -
308A ASN* 4.2 15.6 - - + +
311A PHE* 3.6 35.4 - - + -
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Residues in contact with VAL 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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148A MET* 4.7 6.5 - - + -
151A LEU* 3.6 27.1 - - + +
152A SER* 5.2 0.9 - - - +
191A LYS* 2.9 52.6 + - + +
192A CYS* 3.8 6.7 - - - +
193A SER 3.3 0.2 - - - -
194A VAL* 1.3 73.0 - - - +
196A ARG* 1.3 61.9 + - - +
198A ALA* 3.1 1.9 + - - +
199A PHE* 2.9 57.0 + - + +
259A TRP* 3.6 15.5 - - + -
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Residues in contact with ARG 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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151A LEU* 4.4 11.1 - - + +
180A LEU* 2.9 40.2 + - + +
181A LEU* 4.2 1.7 - - - +
182A ALA 3.0 27.1 + - - -
183A ARG* 3.7 36.2 - - - +
189A ARG* 3.6 6.7 - - - +
192A CYS 2.8 18.7 + - - +
193A SER 3.3 15.9 + - - +
195A VAL* 1.3 76.4 - - - +
197A GLU* 1.3 81.4 + - - +
200A THR* 2.8 42.4 + - - +
202A THR* 3.0 33.3 + - + +
247A MET* 4.6 1.1 - - + -
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Residues in contact with GLU 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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184A PRO* 4.8 5.2 - - - +
189A ARG* 2.9 29.9 + - - -
193A SER 2.7 17.0 + - - +
194A VAL* 3.4 5.8 - - - +
195A VAL 3.1 0.2 - - - -
196A ARG* 1.3 101.8 - - - +
198A ALA* 1.3 61.6 + - - +
200A THR 3.7 9.1 - - - +
250A ILE* 4.2 6.4 - - - +
307A THR* 4.3 8.3 - - - +
308A ASN* 3.2 33.5 + - + +
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Residues in contact with ALA 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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194A VAL 2.8 16.2 + - - +
195A VAL 3.1 4.0 + - - +
197A GLU* 1.3 79.8 - - - +
199A PHE* 1.3 65.8 + - + +
250A ILE* 4.0 11.6 - - - +
252A PHE* 4.2 12.1 - - - +
254A PHE* 4.2 9.9 - - + -
259A TRP* 3.6 17.0 - - + -
308A ASN* 3.3 34.7 + - - +
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Residues in contact with PHE 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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151A LEU* 4.1 8.1 - - + -
152A SER* 5.5 2.9 - - - -
154A ILE* 3.7 17.2 - - + +
155A GLY* 3.6 28.7 - - - -
195A VAL* 2.9 42.8 + - + +
198A ALA* 1.3 78.4 - - + +
200A THR* 1.3 66.3 + - + +
249A PRO* 3.4 2.9 - - - +
250A ILE* 2.9 29.1 + - - +
252A PHE* 3.4 44.2 - + - -
254A PHE* 3.6 14.6 - + - -
256A VAL* 4.3 11.9 - - + -
259A TRP* 3.8 23.6 - + - -
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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