Contacts of the helix formed by residues 164 - 175 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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57B PHE* 3.2 23.9 + - + +
60B ILE* 2.7 35.2 + - + -
62B PHE* 4.4 4.9 - - + -
163B ASN* 1.3 74.0 - - - +
165B ARG* 1.3 56.0 + - - +
167B LEU* 3.7 7.9 - - - +
168B MET* 3.0 39.1 + - + +
194B PHE* 4.1 20.2 - - + -
201B THR* 5.2 0.2 - - + -
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Residues in contact with ARG 165 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54B GLU* 2.8 56.3 + - + +
55B THR* 3.5 11.0 - - - +
57B PHE* 3.7 3.4 + - + -
58B GLU* 2.7 49.1 + - + +
163B ASN* 3.0 9.5 + - - +
164B ALA* 1.3 75.7 - - - +
166B SER* 1.3 64.7 + - - +
168B MET* 3.3 14.8 + - + +
169B ASN* 3.1 21.0 + - - +
80D ARG* 3.4 4.0 - - - +
300D FAD 2.8 77.3 + - + +
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Residues in contact with SER 166 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79B HIS* 5.0 4.9 + - - +
81B ILE* 2.5 46.5 + - - +
82B ALA* 4.8 0.3 - - - +
160B TRP* 5.6 0.5 - - - -
162B VAL* 3.5 14.4 - - - +
163B ASN* 3.0 13.5 + - - -
165B ARG* 1.3 78.4 - - - +
167B LEU* 1.3 55.4 + - - +
169B ASN* 3.3 8.8 + - - +
170B PHE* 2.9 27.4 + - - +
310B FAD 4.1 10.2 + - - -
300D FAD 4.0 3.5 - - - -
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Residues in contact with LEU 167 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62B PHE* 3.7 35.2 - - + -
64B PHE* 4.1 11.0 - - + -
160B TRP* 3.6 24.2 - - + -
162B VAL* 3.7 9.1 - - + +
163B ASN 2.9 17.4 + - - +
164B ALA* 3.7 5.8 - - - +
166B SER* 1.3 76.1 - - - +
168B MET* 1.3 57.9 + - + +
170B PHE* 3.2 7.6 + - + +
171B LEU* 2.9 33.0 + - + +
190B ILE* 3.0 37.0 - - + -
194B PHE* 4.3 22.9 - - + -
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Residues in contact with MET 168 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49B MET* 3.8 14.4 - - + +
54B GLU* 5.5 2.9 - - + +
57B PHE* 3.8 36.6 - - + -
164B ALA* 3.0 31.8 + - + +
165B ARG* 3.3 10.1 + - + +
167B LEU* 1.3 74.6 - - - +
169B ASN* 1.3 59.3 + - - +
171B LEU* 3.4 3.5 + - - +
172B ASN* 3.0 33.3 + - - +
194B PHE* 3.6 25.1 - - + -
201B THR* 4.2 4.3 - - + -
205B PHE* 3.6 50.1 - - + -
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Residues in contact with ASN 169 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79B HIS* 4.3 3.4 + - - -
165B ARG 3.1 13.4 + - - +
166B SER* 3.5 11.4 - - - +
167B LEU 3.3 0.2 - - - -
168B MET* 1.3 72.6 - - - +
170B PHE* 1.3 68.4 + - - +
172B ASN* 3.2 14.5 + - - +
173B LEU* 3.1 33.7 + - - +
211B LYS* 4.8 7.8 + - - -
310B FAD 2.9 62.4 + - - -
300D FAD 5.9 2.2 - - - +
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Residues in contact with PHE 170 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76B TRP* 3.4 49.6 - + - -
79B HIS* 3.5 38.1 - + + +
160B TRP* 3.7 24.2 - + + -
166B SER 2.9 13.6 + - - +
167B LEU* 3.3 11.2 - - + +
169B ASN* 1.3 75.4 - - - +
171B LEU* 1.3 62.4 + - + +
173B LEU* 3.2 1.7 + - - -
174B ARG* 2.7 58.6 + - + +
183B ILE* 4.6 4.7 - - + -
187B ALA* 4.0 22.2 - - + -
190B ILE* 4.0 17.7 - - + -
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Residues in contact with LEU 171 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167B LEU* 2.9 21.8 + - + +
168B MET* 3.9 5.2 - - - +
169B ASN 3.2 0.2 - - - -
170B PHE* 1.3 88.8 - - + +
172B ASN* 1.3 64.0 + - - +
175B ALA* 3.0 32.1 + - + +
187B ALA* 3.2 32.8 - - + +
190B ILE* 4.0 10.5 - - + -
191B ALA* 4.0 18.8 - - + +
194B PHE* 3.8 30.1 - - + -
202B PHE* 4.4 0.9 - - + -
205B PHE* 4.2 20.9 - - + -
210B TYR* 3.7 4.1 - - - -
215B LEU* 4.3 7.4 - - + -
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Residues in contact with ASN 172 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168B MET* 3.0 19.3 + - - +
169B ASN* 3.2 16.8 + - - +
171B LEU* 1.3 76.8 - - - +
173B LEU* 1.3 68.9 + - + +
176B ASP* 3.7 16.5 - - - +
205B PHE* 3.4 5.5 - - - -
209B ALA 4.0 4.9 + - - -
210B TYR* 3.3 17.4 - - - -
211B LYS* 2.7 66.9 + - + +
212B GLY* 4.0 8.7 + - - +
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Residues in contact with LEU 173 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79B HIS* 4.3 9.4 - - + -
169B ASN* 3.1 27.7 + - - +
170B PHE 4.0 1.8 - - - +
172B ASN* 1.3 88.4 - - + +
174B ARG* 1.3 60.2 + - - +
176B ASP* 4.1 6.8 - - - +
179B ALA* 3.6 9.9 + - - +
211B LYS* 6.1 3.8 - - - +
310B FAD 3.0 79.9 - - + +
52D GLY 5.4 7.2 - - - +
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Residues in contact with ARG 174 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75B GLN* 2.8 36.0 + - - +
79B HIS* 3.0 22.4 + - - +
170B PHE* 2.7 46.9 + - + +
173B LEU* 1.3 78.0 - - - +
175B ALA* 1.3 55.1 + - - +
176B ASP 3.0 10.6 + - - -
179B ALA* 3.5 11.3 - - - +
183B ILE* 4.0 25.6 - - + +
184B GLN* 3.3 21.7 - - - -
187B ALA* 3.7 16.4 - - + -
310B FAD 3.5 33.8 + - - +
313C UMP 2.9 40.8 + - - -
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Residues in contact with ALA 175 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171B LEU* 3.0 22.1 + - + +
174B ARG* 1.3 72.8 - - - +
176B ASP* 1.3 59.5 - - - +
187B ALA* 3.6 18.7 - - + +
188B LEU 5.1 0.2 - - - +
210B TYR* 2.5 30.0 + - - -
214B ILE* 3.4 19.0 - - + +
215B LEU* 3.7 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
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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