Contacts of the helix formed by residues 193 - 204 (chain E) in PDB entry 4OMD
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 ARG 193 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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189E MET 5.5 2.7 + - - -
190E ASN* 3.3 28.3 + - + +
191E ASP 3.2 3.3 + - - +
192E ASN* 1.3 76.7 - - - +
194E HIS* 1.3 71.3 + - + +
195E GLY 3.4 1.1 - - - -
196E THR* 3.2 6.7 + - - -
197E ARG* 3.1 69.8 + - - +
355E ASP* 3.6 15.3 + - - +
356E LEU* 3.6 22.4 - - + -
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Residues in contact with HIS 194 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153E ASP* 2.8 28.6 + - - -
154E ASP* 3.1 14.7 + - - +
191E ASP 4.7 0.7 - - - +
193E ARG* 1.3 83.1 - - + +
195E GLY* 1.3 64.4 + - - +
197E ARG* 3.2 9.8 + - - +
198E CYS* 3.2 29.3 + - - -
253E SER* 3.3 26.2 - - - -
364E HIS* 4.4 9.9 - + - -
368E SER* 2.5 36.2 + - - -
4L ARG* 3.4 34.7 - - + +
5L 00S 3.9 0.2 + - - -
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Residues in contact with GLY 195 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151E ILE* 3.9 6.9 - - - +
153E ASP* 3.2 22.6 + - - -
154E ASP* 2.7 18.6 + - - -
155E GLY 3.3 20.4 - - - -
156E ILE* 5.0 0.6 - - - +
194E HIS* 1.3 73.3 - - - +
196E THR* 1.3 55.5 + - - +
198E CYS* 3.3 3.2 + - - +
199E ALA* 3.0 29.1 + - - +
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Residues in contact with THR 196 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154E ASP* 4.5 0.2 + - - -
155E GLY 3.6 2.9 + - - -
156E ILE* 3.8 5.1 - - - +
157E GLU* 3.1 41.4 + - + +
160E HIS* 4.4 1.8 - - + -
163E LEU* 4.2 8.7 - - + -
184E PRO* 3.9 8.8 - - - +
192E ASN 4.6 0.9 + - - -
193E ARG* 3.2 11.3 + - - -
195E GLY* 1.3 77.3 - - - +
197E ARG* 1.3 62.4 + - - +
199E ALA* 3.4 6.5 + - - +
200E GLY 3.2 9.0 + - - -
354E THR* 2.9 38.3 + - - +
355E ASP 4.1 15.5 - - - +
356E LEU* 4.1 8.1 - - - +
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Residues in contact with ARG 197 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193E ARG* 3.1 63.1 + - - +
194E HIS* 3.2 8.7 + - - +
196E THR* 1.3 78.1 - - - +
198E CYS* 1.3 62.0 + - - +
200E GLY 3.4 1.4 + - - -
201E GLU* 3.4 4.5 + - - +
353E THR* 2.7 32.7 + - + +
354E THR 3.1 17.5 - - - +
355E ASP* 2.5 39.8 + - - +
361E THR* 3.6 19.3 + - - +
363E SER* 3.7 22.4 + - - -
364E HIS* 3.6 32.0 + - - +
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Residues in contact with CYS 198 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151E ILE* 4.0 16.2 - - + -
153E ASP* 4.3 3.6 - - - -
194E HIS* 3.2 26.3 + - - -
195E GLY 3.7 6.5 - - - +
197E ARG* 1.3 80.2 - - - +
199E ALA* 1.3 63.5 - - - +
201E GLU* 3.1 26.0 + - - +
202E VAL* 3.5 5.0 + - - +
253E SER* 3.7 29.2 - - - +
364E HIS* 3.9 9.4 - - - -
368E SER 3.8 11.7 - - - -
372E PRO* 3.5 16.8 - - + +
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Residues in contact with ALA 199 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151E ILE* 3.8 20.6 - - + +
156E ILE* 3.8 30.3 - - + -
163E LEU* 4.1 10.8 - - + +
195E GLY 3.0 18.1 + - - +
196E THR 3.7 4.9 - - - +
197E ARG 3.3 0.2 - - - -
198E CYS* 1.3 76.1 - - - +
200E GLY* 1.3 62.7 - - - +
202E VAL* 3.0 14.4 + - - +
203E ALA* 3.0 12.5 + - - -
221E ILE* 4.1 8.5 - - + +
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Residues in contact with GLY 200 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163E LEU* 4.0 12.3 - - - +
196E THR 3.2 8.1 + - - -
197E ARG 3.4 0.2 + - - -
198E CYS 3.3 0.4 - - - -
199E ALA* 1.3 79.6 - - - +
201E GLU* 1.3 60.4 + - - +
204E ALA* 3.0 31.9 + - - +
213E VAL 4.4 1.0 - - - +
214E GLY* 3.5 3.5 - - - -
352E VAL 5.8 0.2 - - - -
353E THR* 3.2 17.7 - - - -
354E THR* 3.3 13.0 + - - -
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Residues in contact with GLU 201 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121E GLN* 6.2 0.9 - - - +
123E TYR* 5.5 0.9 - - + +
197E ARG 3.6 9.2 - - - +
198E CYS* 3.1 9.7 + - - +
200E GLY* 1.3 76.0 - - - +
202E VAL* 1.3 58.4 + - - +
213E VAL 4.6 1.9 - - - +
214E GLY* 3.3 2.4 - - - -
215E VAL* 3.0 30.7 + - - +
351E ILE* 3.5 22.7 - - + +
352E VAL 5.1 1.3 - - - +
353E THR* 3.2 9.2 + - - +
364E HIS* 3.0 31.1 + - - -
369E ALA* 2.5 32.7 - - - +
372E PRO* 3.4 22.2 - - + +
373E LEU* 3.5 20.2 - - + +
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Residues in contact with VAL 202 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149E VAL* 4.0 30.5 - - + -
151E ILE* 3.9 17.7 - - + -
198E CYS 3.6 14.1 - - - +
199E ALA 3.0 4.9 + - - +
201E GLU* 1.3 78.3 - - - +
203E ALA* 1.3 60.2 + - + +
214E GLY* 3.8 1.1 - - - -
215E VAL 3.2 1.8 + - - +
216E ALA* 2.9 34.8 + - + +
219E ALA* 5.6 0.2 - - + -
221E ILE* 4.1 7.6 - - + -
372E PRO* 3.3 28.9 - - + +
375E ALA* 4.4 4.0 - - + -
376E GLY* 3.9 20.4 - - - +
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Residues in contact with ALA 203 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162E ASP 4.2 2.1 - - - +
163E LEU* 4.2 6.2 - - - +
166E ASN* 2.9 18.2 + - - +
199E ALA 3.0 8.0 + - - -
202E VAL* 1.3 85.5 - - + +
204E ALA* 1.3 65.9 + - - +
205E VAL 3.4 0.7 + - - -
214E GLY* 4.1 1.1 - - - -
216E ALA 3.5 18.2 - - - +
217E TYR* 4.5 0.4 - - - -
219E ALA* 3.9 18.4 - - + +
221E ILE* 3.8 25.6 - - + -
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Residues in contact with ALA 204 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162E ASP* 3.3 28.5 - - - +
163E LEU* 4.2 3.6 - - - -
200E GLY* 3.0 28.2 + - - +
203E ALA* 1.3 77.6 - - - +
205E VAL* 1.3 65.9 + - - +
212E GLY 4.3 0.7 - - - +
213E VAL* 3.8 7.2 - - - +
214E GLY* 3.0 25.4 + - - +
217E TYR* 3.4 9.7 - - - +
353E THR* 6.2 1.1 - - - -
354E THR* 4.3 5.4 - - + +
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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