Contacts of the helix formed by residues 193 - 204 (chain F) in PDB entry 4RYD
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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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520C PRO* 5.9 3.0 - - - +
521C HIS* 3.9 31.3 + - - -
189F MET 5.6 1.3 + - - -
190F ASN* 3.4 29.5 + - + +
191F ASP 3.3 2.8 - - - +
192F ASN* 1.3 77.1 - - - +
194F HIS* 1.3 68.9 + - + +
195F GLY 3.5 1.3 - - - -
196F THR* 3.4 6.2 + - - -
197F ARG* 3.0 64.4 + - - +
355F ASP* 3.5 25.2 + - - +
356F LEU* 3.6 22.0 - - + -
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Residues in contact with HIS 194 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153F ASP* 2.7 33.9 + - - +
154F ASP* 3.1 13.9 + - - +
191F ASP 4.4 1.3 + - - +
193F ARG* 1.3 84.0 - - + +
195F GLY* 1.3 62.8 + - - +
197F ARG* 3.2 9.3 + - - +
198F CYS* 3.1 25.9 + - - -
253F SER* 3.2 28.0 - - - -
364F HIS* 4.6 8.3 - + - -
368F SER* 2.7 31.0 + - - -
4N ARG* 3.6 32.2 - - + +
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Residues in contact with GLY 195 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151F ILE* 3.9 7.1 - - - +
153F ASP* 3.1 23.5 + - - -
154F ASP* 2.5 23.9 + - - -
155F GLY 3.3 13.7 - - - -
156F ILE* 5.0 0.9 - - - -
194F HIS* 1.3 72.7 - - - +
196F THR* 1.3 55.3 + - - +
198F CYS* 3.2 3.4 + - - +
199F ALA* 2.9 29.2 + - - +
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Residues in contact with THR 196 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154F ASP* 4.4 0.2 + - - -
155F GLY 3.5 2.9 + - - -
156F ILE* 3.7 4.9 - - - +
157F GLU* 3.0 36.8 + - + +
160F HIS* 4.4 1.8 - - + -
163F LEU* 4.1 13.4 - - + +
184F PRO* 3.9 8.3 - - - +
192F ASN 4.8 0.9 + - - -
193F ARG* 3.4 11.3 + - - -
194F HIS 3.3 0.6 - - - -
195F GLY* 1.3 75.6 - - - +
197F ARG* 1.3 61.1 + - - +
199F ALA* 3.3 7.8 + - - +
200F GLY 3.2 9.2 + - - -
354F THR* 2.9 38.6 + - - +
355F ASP 4.0 17.0 - - - +
356F LEU* 4.2 5.5 - - - +
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Residues in contact with ARG 197 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193F ARG* 3.0 62.1 + - - +
194F HIS* 3.2 9.2 + - - +
196F THR* 1.3 77.3 - - - +
198F CYS* 1.3 62.6 + - - +
201F GLU* 3.5 4.7 - - - +
353F THR* 2.7 35.6 + - + +
354F THR 3.2 18.6 - - - +
355F ASP* 2.8 38.2 + - - +
361F THR* 3.6 20.2 + - + +
363F SER* 3.6 24.7 + - - -
364F HIS* 3.8 28.1 + - + +
365F THR 5.3 0.4 - - - +
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Residues in contact with CYS 198 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151F ILE* 4.1 17.7 - - + -
153F ASP* 4.5 2.2 - - - -
194F HIS* 3.1 27.8 + - - +
195F GLY 3.7 6.3 - - - +
197F ARG* 1.3 77.1 - - - +
199F ALA* 1.3 63.6 + - - +
201F GLU* 3.2 24.9 + - - +
202F VAL* 3.5 5.4 + - - +
251F SER* 5.8 0.2 - - - +
253F SER* 3.7 19.7 - - - +
364F HIS* 3.8 9.4 - - - -
368F SER 3.6 24.2 - - - -
372F PRO* 3.5 15.2 - - + +
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Residues in contact with ALA 199 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151F ILE* 3.8 21.0 - - + +
156F ILE* 3.8 31.6 - - + -
163F LEU* 4.2 8.9 - - + +
195F GLY 2.9 17.2 + - - +
196F THR 3.6 5.2 - - - +
197F ARG 3.3 0.2 - - - -
198F CYS* 1.3 77.8 - - - +
200F GLY* 1.3 62.9 + - - +
202F VAL* 3.1 5.2 + - - +
203F ALA* 3.0 21.3 + - - -
204F ALA 4.2 0.2 + - - -
221F ILE* 4.2 8.1 - - + +
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Residues in contact with GLY 200 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163F LEU* 3.8 11.6 - - - +
196F THR 3.2 8.7 + - - -
197F ARG 3.5 0.2 + - - -
198F CYS 3.3 0.6 - - - -
199F ALA* 1.3 78.6 - - - +
201F GLU* 1.3 61.4 + - - +
204F ALA* 3.0 30.9 + - - +
213F VAL 4.3 1.4 - - - +
214F GLY* 3.4 4.3 - - - -
352F VAL 5.8 0.2 - - - -
353F THR* 3.2 10.0 - - - -
354F THR* 3.1 20.8 + - - -
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Residues in contact with GLU 201 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121F GLN* 6.2 1.1 - - - +
123F TYR* 6.5 0.2 - - - -
197F ARG 3.5 10.5 - - - +
198F CYS* 3.2 8.2 + - - +
200F GLY* 1.3 76.4 - - - +
202F VAL* 1.3 57.9 + - - +
213F VAL 4.7 1.9 - - - +
214F GLY* 3.4 2.2 - - - -
215F VAL* 3.0 30.8 + - - +
351F ILE* 3.6 21.5 - - + +
352F VAL 5.3 2.2 - - - +
353F THR* 3.2 6.6 + - - +
364F HIS* 3.0 32.8 + - + -
369F ALA* 2.5 33.9 - - - +
372F PRO* 3.4 21.6 - - + +
373F LEU* 3.3 21.9 - - + +
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Residues in contact with VAL 202 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149F VAL* 3.9 29.8 - - + -
151F ILE* 4.0 15.5 - - + -
198F CYS 3.6 13.9 - - - +
199F ALA 3.1 5.5 + - - +
201F GLU* 1.3 78.1 - - - +
203F ALA* 1.3 62.1 + - + +
214F GLY* 3.8 1.3 - - - -
215F VAL* 3.2 1.3 + - - +
216F ALA* 2.9 33.6 + - + +
219F ALA* 5.5 0.4 - - + -
221F ILE* 4.1 8.1 - - + -
372F PRO* 3.3 31.0 - - + +
375F ALA* 4.4 4.7 - - + -
376F GLY* 4.0 19.1 - - - +
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Residues in contact with ALA 203 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162F ASP 4.2 1.6 - - - +
163F LEU* 4.5 5.8 - - - +
166F ASN* 2.9 18.7 + - - +
199F ALA 3.0 9.6 + - - -
202F VAL* 1.3 85.9 - - + +
204F ALA* 1.3 66.8 + - - +
205F VAL 3.3 0.9 + - - -
214F GLY* 4.0 1.6 - - - -
216F ALA 3.4 17.5 - - - +
219F ALA* 4.0 16.6 - - + +
221F ILE* 3.9 26.4 - - + +
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Residues in contact with ALA 204 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162F ASP* 3.2 29.2 - - - +
163F LEU* 4.2 3.8 - - - -
200F GLY* 3.0 27.7 + - - +
203F ALA* 1.3 75.6 - - - +
205F VAL* 1.3 65.0 + - - +
211F CYS* 6.4 0.2 - - - -
212F GLY 4.3 0.9 - - - +
213F VAL* 3.9 7.0 - - - +
214F GLY* 3.0 25.7 + - - +
217F TYR* 3.4 9.7 - - - +
353F THR* 6.2 1.3 - - - -
354F THR* 4.4 5.8 - - + +
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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