Contacts of the helix formed by residues 164 - 182 (chain C) in PDB entry 6M04
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 TYR 164 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154C TYR* 5.7 0.9 - - - -
155C HIS* 5.9 2.1 + - - -
160C TRP* 3.3 28.5 + - + +
163C LYS* 1.3 114.1 - - + +
165C PHE* 1.3 62.6 + - - +
166C PRO* 3.6 3.8 - - - -
167C TYR* 3.6 33.8 + + + +
168C LEU* 3.9 5.2 + - - +
360D TYR* 4.0 21.7 - - + +
361D MET* 3.6 38.0 + - + +
364D LYS* 3.6 34.1 - - + -
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Residues in contact with PHE 165 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42C ALA* 6.4 1.3 - - + -
160C TRP 4.5 1.0 + - - -
161C TYR* 3.9 26.0 - - + +
162C SER 5.7 0.2 - - - -
163C LYS 3.5 1.5 - - - +
164C TYR* 1.3 73.6 - - - +
166C PRO* 1.4 77.9 - - + +
167C TYR 3.1 2.7 - - - -
168C LEU* 3.1 23.9 + - + +
169C ALA* 3.1 28.8 + - + -
325C TYR* 5.7 1.8 - + - -
326C THR* 3.8 26.5 - - + -
329C PHE* 5.4 11.7 - + + -
362C LEU* 5.3 17.9 - - + -
366C LEU* 3.6 38.6 - - + -
369C TYR* 4.6 12.1 - + - -
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Residues in contact with PRO 166 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39C ALA* 3.8 21.9 - - + +
40C ILE* 5.8 0.7 - - - +
42C ALA* 3.9 15.5 - - + +
43C GLY* 3.7 27.4 - - - +
46C GLN* 5.1 11.7 - - + +
163C LYS 4.6 7.0 - - - +
164C TYR* 3.8 2.9 - - - -
165C PHE* 1.4 95.5 - - + +
167C TYR* 1.3 64.9 + - + +
169C ALA* 3.6 9.6 - - + +
170C LEU* 2.9 27.9 + - - +
362C LEU* 5.6 7.0 - - + -
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Residues in contact with TYR 167 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43C GLY* 5.7 5.4 - - - -
46C GLN* 5.8 0.6 + - - -
47C LEU* 5.3 6.1 - - - +
163C LYS 5.5 0.9 - - - -
164C TYR* 3.6 29.1 + + + +
165C PHE 3.1 1.4 - - - -
166C PRO* 1.3 84.0 - - + +
168C LEU* 1.3 60.4 + - - +
170C LEU* 3.2 17.9 + - + +
171C ILE* 3.0 33.6 + - + +
41D PHE* 3.7 29.0 - + - -
361D MET* 3.8 32.8 - - + +
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Residues in contact with LEU 168 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164C TYR 3.9 5.0 + - - +
165C PHE* 3.1 27.4 + - + +
167C TYR* 1.3 80.5 - - - +
169C ALA* 1.3 62.7 + - - +
171C ILE* 3.3 17.3 + - + +
172C HIS* 3.0 25.3 + - + +
322C ILE* 5.8 6.3 - - + -
325C TYR* 3.7 39.5 - - + +
326C THR* 5.2 3.8 - - + -
369C TYR* 5.9 1.3 - - - +
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Residues in contact with ALA 169 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35C MET* 4.3 1.4 - - - +
39C ALA* 3.7 20.4 - - + -
165C PHE* 3.1 21.5 + - + +
166C PRO* 3.6 11.2 - - + +
167C TYR 3.3 0.4 - - - -
168C LEU* 1.3 79.3 - - - +
170C LEU* 1.3 51.7 + - - +
172C HIS* 3.3 5.0 + - - +
173C THR* 2.7 37.6 + - - -
369C TYR* 4.2 27.8 - - + +
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Residues in contact with LEU 170 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3C THR* 5.8 6.1 - - + +
39C ALA* 4.5 4.0 - - - +
40C ILE* 4.0 27.4 - - + -
166C PRO 2.9 14.3 + - - +
167C TYR* 3.3 19.3 - - + +
169C ALA* 1.3 76.6 - - - +
171C ILE* 1.3 79.9 + - + +
173C THR* 3.2 8.6 + - - -
174C ILE* 3.0 39.2 + - + +
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Residues in contact with ILE 171 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167C TYR* 3.0 17.4 + - + +
168C LEU* 3.3 17.9 + - + +
170C LEU* 1.3 89.8 - - + +
172C HIS* 1.3 63.4 + - - +
174C ILE* 3.3 8.5 + - + +
175C ILE* 3.0 36.9 + - + +
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Residues in contact with HIS 172 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35C MET* 3.5 25.4 - - + +
168C LEU* 3.0 16.9 + - + +
169C ALA 3.7 7.0 - - - +
171C ILE* 1.3 77.9 - - - +
173C THR* 1.3 57.1 + - - +
175C ILE* 3.4 9.7 + - + +
176C LEU* 2.9 42.7 + - + +
318C LYS* 4.2 23.0 - - + +
319C PHE* 5.6 0.9 - - - -
322C ILE* 3.3 52.3 - - + +
369C TYR* 3.9 10.1 - + - +
373C ILE* 5.0 5.2 - - + +
376C TYR* 5.9 2.3 - + - -
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Residues in contact with THR 173 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32C ALA* 4.2 9.5 - - + +
35C MET* 3.0 31.8 - - + -
36C LEU* 3.7 44.0 - - + -
39C ALA* 4.7 1.6 - - - +
169C ALA 2.7 22.2 + - - -
170C LEU* 3.2 10.7 + - - -
172C HIS* 1.3 77.7 - - - +
174C ILE* 1.3 58.9 + - + +
176C LEU* 3.2 2.7 + - - +
177C MET* 2.9 29.4 + - + +
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Residues in contact with ILE 174 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36C LEU* 5.6 7.0 - - + -
170C LEU* 3.0 26.7 + - + +
171C ILE* 3.7 11.0 - - + +
173C THR* 1.3 77.3 - - + +
175C ILE* 1.3 69.9 + - + +
177C MET* 3.3 19.0 + - + +
178C VAL* 3.1 34.1 + - + +
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Residues in contact with ILE 175 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171C ILE* 3.0 28.2 + - + +
172C HIS* 3.7 10.5 - - + +
174C ILE* 1.3 78.8 - - + +
176C LEU* 1.3 58.3 + - - +
178C VAL* 3.4 7.8 + - + +
179C SER* 3.0 31.0 + - - -
314C ILE* 6.1 4.5 - - + -
318C LYS* 5.2 15.3 - - + -
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Residues in contact with LEU 176 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28C MET 5.4 0.2 - - - +
31C LEU* 6.1 0.9 - - + -
32C ALA* 4.0 26.0 - - + -
35C MET* 4.3 13.0 - - + -
172C HIS* 2.9 34.9 + - + +
173C THR* 3.2 6.7 + - - +
175C ILE* 1.3 77.1 - - + +
177C MET* 1.3 57.0 + - - +
179C SER* 2.8 27.1 + - - +
180C SER* 2.9 18.4 + - - -
314C ILE 5.5 2.7 - - - +
315C LYS* 5.6 4.7 - - - +
318C LYS* 5.3 9.4 - - + -
373C ILE* 5.7 2.9 - - + -
376C TYR* 3.3 45.5 - - + +
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Residues in contact with MET 177 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8C ALA* 5.0 3.4 - - - +
11C ASN* 3.6 54.7 - - + +
12C ASP* 3.5 33.0 - - - +
173C THR* 2.9 17.8 + - + +
174C ILE* 3.6 20.2 - - - +
176C LEU* 1.3 75.3 - - - +
178C VAL* 1.3 64.2 + - + +
180C SER* 2.5 23.5 + - - -
181C ASN* 3.1 16.7 + - - +
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Residues in contact with VAL 178 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174C ILE* 3.1 27.3 + - + +
175C ILE* 3.9 7.6 - - + +
177C MET* 1.3 78.9 - - + +
179C SER* 1.3 58.0 + - - +
181C ASN* 3.2 3.9 + - - +
182C PHE* 3.0 38.5 + - + +
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Residues in contact with SER 179 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175C ILE* 3.0 18.1 + - - -
176C LEU* 2.8 35.2 + - - +
178C VAL* 1.3 76.3 - - - +
180C SER* 1.3 56.9 + - - +
182C PHE* 3.5 9.5 - - - -
311C GLN* 2.7 33.8 + - - +
314C ILE* 3.7 37.3 + - - +
315C LYS* 5.9 0.3 - - - -
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Residues in contact with SER 180 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12C ASP* 3.7 14.7 + - - -
25C ASP* 4.2 19.2 - - - +
28C MET* 6.3 3.1 - - - -
29C ASP* 5.9 9.9 - - - -
176C LEU* 2.9 14.2 + - - -
177C MET* 2.5 26.6 + - - -
179C SER* 1.3 79.9 + - - +
181C ASN* 1.3 63.3 + - - +
182C PHE 3.6 0.2 - - - -
183C TRP* 4.5 4.2 + - - +
184C PHE* 6.0 2.4 - - - -
311C GLN* 4.2 10.7 + - - +
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Residues in contact with ASN 181 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11C ASN 4.8 1.4 + - - -
12C ASP* 3.3 23.5 + - - +
13C ILE 3.8 25.8 + - - +
14C GLN* 4.4 10.2 - - - +
29C ASP* 5.4 0.5 - - - +
177C MET* 3.1 25.5 + - - +
178C VAL* 3.2 3.8 + - - +
180C SER* 1.3 85.7 + - - +
182C PHE* 1.3 61.4 + - - +
183C TRP 3.1 6.9 + - - -
184C PHE* 3.6 5.0 + - - -
185C LYS* 3.1 40.0 + - + +
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Residues in contact with PHE 182 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178C VAL* 3.0 32.3 + - + +
179C SER* 3.5 8.7 - - - -
180C SER 3.6 0.4 - - - -
181C ASN* 1.3 76.3 - - - +
183C TRP* 1.3 63.4 + - - +
184C PHE 3.2 0.7 - - - -
185C LYS* 4.0 5.4 - - - +
186C TYR* 3.2 31.8 - + + -
307C LEU* 4.6 4.9 - - + +
310C VAL* 3.7 34.8 - - + -
311C GLN* 3.2 25.8 - - - -
314C ILE* 3.8 34.1 - - + -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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