Contacts of the helix formed by residues 164 - 175 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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57A PHE* 3.1 25.1 + - + +
60A ILE* 2.9 29.3 + - + -
62A PHE* 4.5 5.5 - - + -
163A ASN* 1.3 72.6 - - - +
165A ARG* 1.3 55.6 + - - +
167A LEU* 3.4 8.1 - - - +
168A MET* 2.9 36.3 + - + +
194A PHE* 4.0 22.8 - - + -
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Residues in contact with ARG 165 (chain A).
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 5.7 0.8 + - - -
54A GLU* 3.0 59.6 + - + +
55A THR* 3.6 12.3 - - - +
57A PHE 3.6 3.4 + - - -
58A GLU* 2.7 46.6 + - + +
163A ASN* 3.2 9.5 + - - +
164A ALA* 1.3 75.7 - - - +
166A SER* 1.3 66.4 + - - +
168A MET* 3.3 15.6 + - + +
169A ASN* 3.2 19.4 + - - +
80C ARG* 3.5 3.2 - - - +
305C FAD 2.9 74.2 + - + +
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Residues in contact with SER 166 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79A HIS* 5.3 5.0 + - - +
81A ILE* 2.7 46.1 + - - +
82A ALA* 4.7 0.5 - - - +
160A TRP* 5.5 0.2 - - - -
162A VAL* 3.5 16.3 - - - +
163A ASN* 3.0 16.2 + - - -
165A ARG* 1.3 75.6 - - - +
167A LEU* 1.3 56.8 + - - +
169A ASN* 3.1 11.3 + - - +
170A PHE* 2.9 27.4 + - - +
315A FAD 4.3 9.1 + - - -
305C FAD 4.1 4.6 - - - -
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Residues in contact with LEU 167 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62A PHE* 3.7 33.9 - - + -
64A PHE* 4.1 24.0 - - + -
160A TRP* 5.1 1.3 - - + -
162A VAL* 3.7 14.1 - - + +
163A ASN 2.9 15.9 + - - +
164A ALA 3.4 6.3 - - - +
166A SER* 1.3 75.9 - - - +
168A MET* 1.3 56.9 + - - +
170A PHE* 3.1 9.0 + - + +
171A LEU* 2.9 43.7 + - + +
190A ILE* 4.0 13.5 - - + -
194A PHE* 3.3 39.5 - - + -
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Residues in contact with MET 168 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49A MET* 3.6 24.9 - - + +
54A GLU* 5.8 3.6 - - + -
57A PHE* 3.9 26.0 - - + -
164A ALA* 2.9 34.4 + - + +
165A ARG* 3.3 14.1 + - + +
167A LEU* 1.3 76.2 - - - +
169A ASN* 1.3 57.4 + - - +
171A LEU* 3.4 0.8 + - - -
172A ASN* 2.9 35.2 + - - +
194A PHE* 3.7 13.7 - - + -
201A THR* 4.3 9.4 - - + -
205A PHE* 3.3 49.1 - - + -
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Residues in contact with ASN 169 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79A HIS* 4.0 5.3 + - - -
165A ARG 3.2 11.2 + - - +
166A SER* 3.1 13.6 + - - +
168A MET* 1.3 74.1 - - - +
170A PHE* 1.3 65.7 + - - +
172A ASN* 3.3 15.3 + - - +
173A LEU* 3.1 34.8 + - - +
315A FAD 3.1 62.4 + - - -
305C FAD 6.0 1.1 - - - +
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Residues in contact with PHE 170 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76A TRP* 3.6 50.5 - + - -
79A HIS* 3.7 36.3 - + + +
160A TRP* 3.8 20.2 - + + -
166A SER 2.9 12.8 + - - +
167A LEU* 3.3 12.1 - - - +
169A ASN* 1.3 77.9 - - - +
171A LEU* 1.3 66.7 + - + +
173A LEU* 3.3 1.0 + - - -
174A ARG* 2.8 49.9 + - + +
183A ILE* 4.6 5.2 - - + -
187A ALA* 4.0 26.9 - - + -
190A ILE* 4.2 15.3 - - + -
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Residues in contact with LEU 171 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167A LEU* 2.9 40.3 + - + +
168A MET 3.9 3.4 - - - +
170A PHE* 1.3 79.1 - - + +
172A ASN* 1.3 64.7 + - - +
175A ALA* 2.9 37.3 + - + +
187A ALA* 3.2 33.2 - - + +
190A ILE* 4.1 9.6 - - + -
191A ALA* 3.8 28.7 - - + +
194A PHE* 4.0 11.2 - - + -
202A PHE* 4.5 1.3 - - + -
205A PHE* 4.1 21.3 - - + -
210A TYR* 3.8 3.9 - - - -
215A LEU* 4.3 3.6 - - + -
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Residues in contact with ASN 172 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168A MET* 2.9 22.5 + - - +
169A ASN* 3.4 16.1 + - - +
171A LEU* 1.3 77.3 - - - +
173A LEU* 1.3 63.3 + - + +
176A ASP* 3.8 14.9 - - - +
205A PHE* 3.4 17.9 - - - -
209A ALA* 4.3 9.1 + - - +
210A TYR* 3.5 2.0 - - - -
211A LYS* 2.9 41.9 + - + +
212A GLY* 3.9 14.9 + - - +
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Residues in contact with LEU 173 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79A HIS* 3.7 12.6 - - + -
169A ASN* 3.1 22.5 + - - +
170A PHE 3.9 2.2 - - - +
172A ASN* 1.3 81.6 - - + +
174A ARG* 1.3 65.8 + - + +
176A ASP* 3.8 9.1 - - - +
179A ALA* 3.5 10.0 + - - +
315A FAD 3.2 80.6 - - + +
52C GLY 5.2 9.4 - - - +
53C HIS* 6.3 2.9 - - + -
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Residues in contact with ARG 174 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75A GLN* 2.8 33.9 + - - +
79A HIS* 3.0 23.0 + - - +
170A PHE* 2.8 43.3 + - + +
173A LEU* 1.3 77.3 - - + +
175A ALA* 1.3 58.8 + - - +
176A ASP 2.9 11.3 + - - -
179A ALA* 3.7 6.5 - - - +
183A ILE* 3.8 24.2 - - + +
184A GLN* 3.4 25.1 - - - +
187A ALA* 3.5 15.9 - - + -
315A FAD 3.6 29.3 + - - +
318D UMP 2.8 47.7 + - - -
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Residues in contact with ALA 175 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171A LEU* 2.9 28.8 + - + +
174A ARG* 1.3 73.8 - - - +
176A ASP* 1.3 59.7 + - - +
187A ALA* 3.4 17.5 - - + +
210A TYR* 2.6 27.3 + - - +
212A GLY* 3.7 0.9 - - - -
214A ILE* 3.6 17.4 - - + +
215A LEU* 3.8 32.1 - - + -
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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