Contacts of the helix formed by residues 164 - 175 (chain C) in PDB entry 3G4C
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 ALA 164 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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57C PHE* 3.2 22.1 + - + +
60C ILE* 2.9 29.4 + - + +
61C VAL* 4.8 0.2 - - - +
62C PHE* 4.6 4.2 - - + -
163C ASN* 1.3 74.3 - - - +
165C ARG* 1.3 57.5 + - - +
167C LEU* 3.7 9.3 - - - +
168C MET* 2.8 38.3 + - + +
194C PHE* 4.1 24.2 - - + -
201C THR* 5.3 0.9 - - + -
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Residues in contact with ARG 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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80A ARG* 3.4 4.4 - - - +
169A ASN* 5.5 0.2 + - - -
315A FAD 3.0 72.9 + - + +
52C GLY 5.3 1.2 + - - -
54C GLU* 2.7 60.7 + - + +
55C THR* 3.5 8.8 - - - +
57C PHE 3.6 3.4 + - - -
58C GLU* 2.8 48.4 + - + +
163C ASN* 2.6 18.5 + - - +
164C ALA* 1.3 71.8 - - - +
166C SER* 1.3 63.2 + - - +
168C MET* 3.2 22.4 + - + +
169C ASN* 3.3 12.0 + - - +
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Residues in contact with SER 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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315A FAD 3.9 5.1 - - - -
79C HIS* 4.9 4.2 + - - +
81C ILE* 2.3 49.2 + - - +
82C ALA* 4.7 0.5 - - - +
160C TRP* 5.4 0.9 - - - -
162C VAL* 3.6 13.1 - - - +
163C ASN* 2.7 16.1 + - - -
165C ARG* 1.3 73.4 - - - +
167C LEU* 1.4 56.7 + - - +
169C ASN* 3.5 10.6 + - - +
170C PHE* 3.1 25.5 + - - +
305C FAD 4.1 8.4 + - - -
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Residues in contact with LEU 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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62C PHE* 3.8 35.9 - - + -
64C PHE* 4.4 8.1 - - + -
160C TRP* 3.9 20.0 - - + -
162C VAL* 3.4 10.0 - - + +
163C ASN 2.8 16.6 + - - +
164C ALA* 3.7 7.0 - - - +
166C SER* 1.4 77.4 - - - +
168C MET* 1.3 57.8 + - - +
170C PHE* 3.3 5.9 + - + +
171C LEU* 3.0 26.2 + - + +
190C ILE* 3.0 37.5 - - + -
194C PHE* 4.2 24.5 - - + -
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Residues in contact with MET 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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49C MET* 3.9 26.9 - - + +
54C GLU* 5.4 5.4 - - + +
57C PHE* 3.9 27.6 - - + -
164C ALA 2.8 30.8 + - - +
165C ARG* 3.2 19.5 + - + +
167C LEU* 1.3 75.0 - - - +
169C ASN* 1.3 58.3 + - - +
171C LEU* 3.3 4.1 + - - +
172C ASN* 2.9 35.0 + - - +
194C PHE* 3.6 27.1 - - + -
201C THR* 4.2 1.8 - - + -
205C PHE* 3.6 35.4 - - + -
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Residues in contact with ASN 169 (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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315A FAD 5.9 0.9 - - - +
79C HIS* 4.1 5.5 + - - -
165C ARG 3.3 10.0 + - - +
166C SER* 3.5 13.2 + - - +
168C MET* 1.3 71.9 - - - +
170C PHE* 1.3 67.6 + - - +
172C ASN* 3.1 20.6 + - - +
173C LEU* 3.2 32.6 + - - +
211C LYS* 5.7 2.6 + - - -
305C FAD 2.9 64.3 + - - -
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Residues in contact with PHE 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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76C TRP* 3.6 43.1 - + - -
79C HIS* 3.6 37.2 - + - +
160C TRP* 3.9 20.6 - + + -
166C SER 3.1 12.5 + - - +
167C LEU* 3.3 18.6 + - + +
169C ASN* 1.3 78.4 - - - +
171C LEU* 1.3 62.6 + - + +
173C LEU* 3.8 0.2 - - - +
174C ARG* 2.8 55.1 + - + +
183C ILE* 4.4 7.2 - - + -
187C ALA* 4.0 20.6 - - + -
190C ILE* 3.9 21.5 - - + -
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Residues in contact with LEU 171 (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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167C LEU* 3.0 19.9 + - + +
168C MET* 3.7 6.7 - - - +
169C ASN 3.2 0.4 - - - -
170C PHE* 1.3 79.1 - - + +
172C ASN* 1.3 65.8 + - - +
175C ALA* 2.9 34.8 + - + +
187C ALA* 3.2 39.3 - - + +
190C ILE* 4.1 9.4 - - + -
191C ALA* 3.8 18.6 - - + +
194C PHE* 3.8 29.4 - - + -
202C PHE* 4.6 0.7 - - + -
205C PHE* 4.1 13.0 - - + -
210C TYR* 3.6 3.0 - - - -
215C LEU* 4.1 20.0 - - + -
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Residues in contact with ASN 172 (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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168C MET* 2.9 21.3 + - - +
169C ASN* 3.1 14.2 + - - +
171C LEU* 1.3 76.4 - - - +
173C LEU* 1.3 63.6 + - + +
176C ASP* 3.6 17.7 - - - +
205C PHE* 3.9 7.9 - - - -
209C ALA 3.8 9.1 + - - -
210C TYR* 3.1 15.5 - - - -
211C LYS* 2.5 61.7 + - + +
212C GLY* 3.6 9.2 + - - -
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Residues in contact with LEU 173 (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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52A GLY 5.2 8.7 - - - +
79C HIS* 3.3 19.1 - - + -
169C ASN* 3.2 27.3 + - - +
170C PHE 3.8 2.0 - - - +
171C LEU 3.1 0.4 - - - -
172C ASN* 1.3 83.1 - - + +
174C ARG* 1.3 65.6 + - - +
176C ASP* 3.9 9.9 - - - +
179C ALA* 3.6 7.6 + - - +
305C FAD 3.1 76.7 - - + +
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Residues in contact with ARG 174 (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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308B UMP 2.9 39.6 + - - -
75C GLN* 2.7 37.9 + - - +
79C HIS* 3.1 23.9 + - - +
170C PHE* 2.8 41.4 + - + +
173C LEU* 1.3 82.9 - - + +
175C ALA* 1.3 52.5 + - - +
176C ASP 2.7 23.2 + - - +
179C ALA* 3.7 7.5 - - - +
183C ILE* 3.9 25.5 - - + +
184C GLN* 3.6 17.8 - - - -
187C ALA* 3.8 15.7 - - + -
305C FAD 3.3 32.7 + - - +
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Residues in contact with ALA 175 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171C LEU* 2.9 25.9 + - + +
174C ARG* 1.3 69.3 - - - +
176C ASP* 1.3 59.8 + - - +
187C ALA* 3.6 18.5 - - + +
210C TYR* 2.5 31.4 + - - +
214C ILE* 3.4 19.4 - - + +
215C LEU* 3.7 33.7 - - + -
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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