Contacts of the helix formed by residues 160 - 170 (chain C) in PDB entry 1REP
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 PRO 160 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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31C LEU 3.6 24.2 - - - +
32C SER* 4.1 14.6 - - - +
33C ARG* 4.4 8.3 - - + +
36C LYS* 4.3 6.2 - - + +
158C THR 3.3 8.9 - - - +
159C ASN* 1.3 87.2 - - - +
161C TYR* 1.3 73.6 + - + +
163C MET* 3.5 16.5 + - + +
164C ARG* 3.2 25.1 + - - +
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Residues in contact with TYR 161 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35B T 5.0 0.4 - - - -
36B G 3.2 34.9 + - - -
30C SER* 4.8 9.8 + - - -
31C LEU 5.9 1.6 - - - -
159C ASN* 2.6 31.4 + - - +
160C PRO* 1.3 83.0 - - + +
162C ALA* 1.3 57.2 + - - +
164C ARG* 3.0 10.9 + - + +
165C LEU* 2.9 26.3 + - - +
192C TYR* 3.3 30.3 - - + -
193C GLN 3.6 10.7 + - - -
194C LEU* 3.4 18.6 - - + -
195C PRO* 3.7 19.0 - - + +
198C TYR* 5.3 2.2 - + - -
207C ARG 6.1 0.9 - - - -
208C PHE* 4.0 23.6 - + + -
212C CYS* 3.9 5.6 - - - -
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Residues in contact with ALA 162 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157C ILE* 3.9 10.4 - - + +
159C ASN* 2.9 12.4 + - + +
161C TYR* 1.3 77.5 - - - +
163C MET* 1.3 63.1 + - - +
165C LEU* 3.7 3.1 - - - +
166C TYR* 3.1 25.6 + - - +
212C CYS* 3.5 36.4 - - + +
215C GLU* 3.9 21.5 - - + +
216C ILE* 3.8 6.9 - - + +
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Residues in contact with MET 163 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33C ARG* 3.7 31.6 - - + +
36C LYS* 3.6 31.6 - - + -
37C ARG* 4.6 9.0 - - + +
40C TYR* 3.4 37.0 + - + +
154C THR* 4.3 13.1 - - - +
157C ILE* 3.3 29.6 - - + +
159C ASN 3.2 7.5 + - - +
160C PRO* 3.6 10.5 - - + +
161C TYR 3.2 0.2 - - - -
162C ALA* 1.3 77.1 - - - +
164C ARG* 1.3 58.0 + - - +
166C TYR* 4.0 4.8 - - - +
167C GLU* 2.9 34.4 + - - +
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Residues in contact with ARG 164 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24C LEU 4.2 1.0 + - - -
25C THR* 3.0 30.7 + - - +
26C GLU 4.2 2.6 - - - -
27C ALA 2.3 32.4 + - - -
29C TYR* 3.6 31.7 + - + +
36C LYS* 3.6 22.2 - - + +
160C PRO 3.2 13.7 + - - +
161C TYR* 3.0 17.8 + - + +
163C MET* 1.3 79.8 - - - +
165C LEU* 1.3 65.3 + - - +
167C GLU* 3.4 8.3 + - - +
168C SER* 3.1 15.6 + - - -
191C ARG* 2.6 27.2 + - - +
192C TYR* 3.5 45.4 + - + +
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Residues in contact with LEU 165 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161C TYR 2.9 11.5 + - - +
162C ALA* 3.4 9.4 + - - +
164C ARG* 1.3 74.6 - - - +
166C TYR* 1.3 52.2 + - - +
168C SER* 2.8 9.2 + - - -
169C LEU* 2.8 51.3 + - + +
183C LEU* 4.2 11.0 - - + -
188C ILE* 5.8 0.4 - - + -
192C TYR* 3.8 11.1 - - + +
208C PHE* 4.5 17.3 - - + -
209C LEU* 5.3 1.8 - - + -
212C CYS* 4.1 22.4 - - + -
213C VAL* 5.1 4.7 - - + -
216C ILE* 4.3 11.9 - - + -
224C LEU* 5.0 3.4 - - + -
240C PHE* 3.8 45.1 - - + -
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Residues in contact with TYR 166 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149C PHE* 4.8 0.9 - + + -
153C GLU* 2.6 46.8 + - + +
154C THR* 3.7 18.4 - - + -
157C ILE* 4.2 5.4 - - + -
162C ALA 3.1 14.1 + - - +
163C MET 4.0 5.2 - - - +
165C LEU* 1.3 78.4 - - - +
167C GLU* 1.3 58.3 + - - +
169C LEU* 3.2 7.8 + - - +
170C CYS* 2.8 49.1 + - - -
173C ARG* 4.3 1.0 + - - -
216C ILE* 3.7 24.1 - - + +
220C THR* 3.0 36.8 - - + -
221C PRO* 3.3 12.8 - - - +
222C MET* 3.9 19.0 - - + +
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Residues in contact with GLU 167 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20C GLN* 3.0 26.4 + - - +
25C THR* 3.9 11.4 - - + +
29C TYR* 4.4 4.0 + - - -
36C LYS* 3.1 29.1 + - - -
40C TYR* 2.3 39.0 + - - +
147C THR* 3.5 10.2 - - + +
149C PHE* 4.1 15.5 - - + -
154C THR* 5.1 4.3 - - + -
163C MET 2.9 19.3 + - - +
164C ARG* 3.7 7.8 - - - +
165C LEU 3.2 0.8 - - - -
166C TYR* 1.3 77.4 - - - +
168C SER* 1.3 62.7 + - - +
170C CYS* 3.2 11.0 + - - +
171C GLN* 3.2 16.6 + - - +
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Residues in contact with SER 168 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25C THR* 4.2 16.5 + - - -
164C ARG 3.1 6.1 + - - -
165C LEU* 2.8 8.1 + - - -
167C GLU* 1.3 74.4 - - - +
169C LEU* 1.3 59.7 + - - -
171C GLN* 2.8 32.6 + - - +
172C TYR* 3.2 15.9 - - - -
181C VAL* 5.9 0.2 - - - -
183C LEU* 4.9 11.1 - - - +
187C TRP* 3.6 16.6 - - - -
192C TYR* 2.7 29.3 + - - -
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Residues in contact with LEU 169 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165C LEU* 2.8 31.7 + - + +
166C TYR* 3.5 12.6 - - - +
168C SER* 1.3 71.8 - - - +
170C CYS* 1.3 57.0 + - - +
172C TYR* 2.9 19.8 + - - -
173C ARG 3.3 0.5 + - - -
181C VAL* 3.8 14.1 - - + -
183C LEU* 5.2 1.6 - - + -
216C ILE* 4.5 5.4 - - + -
222C MET* 3.6 24.0 - - + -
224C LEU* 3.2 31.0 - - + -
240C PHE* 3.7 35.4 - - + -
242C PHE* 3.0 33.9 - - + -
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Residues in contact with CYS 170 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147C THR* 3.9 15.9 - - + +
148C GLN* 4.0 9.3 + - - +
149C PHE* 4.0 10.5 - - + -
166C TYR* 2.8 48.4 + - - -
167C GLU* 3.4 11.9 - - - +
168C SER 3.1 0.2 - - - -
169C LEU* 1.3 71.9 - - - +
171C GLN* 1.3 59.1 + - - +
172C TYR 3.0 6.4 + - - -
173C ARG* 3.4 49.9 + - - +
222C MET* 4.5 3.1 - - - -
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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