Contacts of the helix formed by residues 164 - 175 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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57D PHE* 3.0 28.0 + - + +
60D ILE* 3.0 29.0 + - + -
62D PHE* 4.6 5.1 - - - -
163D ASN* 1.3 72.5 - - - +
165D ARG* 1.3 55.4 + - - +
167D LEU* 3.3 8.0 + - - +
168D MET* 2.8 36.7 + - + +
194D PHE* 4.1 22.4 - - + -
201D THR* 5.3 0.2 - - + -
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Residues in contact with ARG 165 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80B ARG* 3.4 4.2 - - - +
310B FAD 2.8 74.8 + - + +
52D GLY 5.6 0.8 + - - -
54D GLU* 2.8 61.1 + - + +
55D THR* 3.7 8.5 - - - +
57D PHE 3.7 2.8 + - - -
58D GLU* 2.6 48.1 + - + +
163D ASN* 3.2 8.9 + - - +
164D ALA* 1.3 75.4 - - - +
166D SER* 1.3 65.7 + - - +
168D MET* 3.2 14.5 + - + +
169D ASN* 3.1 20.8 + - - +
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Residues in contact with SER 166 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310B FAD 4.0 13.2 - - - -
79D HIS* 5.2 4.0 + - - +
81D ILE* 2.5 37.6 + - - +
82D ALA* 4.8 0.5 - - - +
160D TRP* 5.6 0.7 - - - -
162D VAL* 3.6 14.3 - - - +
163D ASN* 2.9 18.7 + - - -
165D ARG* 1.3 72.2 - - - +
167D LEU* 1.3 56.9 + - - +
169D ASN* 3.2 9.5 + - - +
170D PHE* 2.9 28.8 + - - +
300D FAD 3.9 12.0 + - - -
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Residues in contact with LEU 167 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62D PHE* 3.9 32.3 - - + -
64D PHE* 4.4 8.3 - - + -
160D TRP* 3.8 20.4 - - + -
162D VAL* 3.5 8.9 - - + +
163D ASN 2.8 22.1 + - - +
164D ALA* 3.4 5.8 - - - +
166D SER* 1.3 74.5 - - - +
168D MET* 1.3 56.7 + - - +
170D PHE* 3.3 5.5 + - + +
171D LEU* 3.0 28.8 + - + +
190D ILE* 2.9 37.0 - - + -
194D PHE* 4.0 26.0 - - + -
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Residues in contact with MET 168 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49D MET* 3.8 18.8 - - + +
54D GLU* 5.8 3.1 - - + -
57D PHE* 3.8 30.7 - - + -
164D ALA* 2.8 36.7 + - + +
165D ARG* 3.2 14.3 + - + +
167D LEU* 1.3 69.6 - - - +
169D ASN* 1.3 61.8 + - - +
171D LEU* 3.4 2.4 + - - +
172D ASN* 2.9 36.1 + - - +
194D PHE* 3.8 17.5 - - + -
201D THR* 4.2 8.1 - - + -
205D PHE* 3.5 46.0 - - + -
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Residues in contact with ASN 169 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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310B FAD 5.9 1.8 - - - +
79D HIS* 3.9 7.7 + - - -
165D ARG 3.1 12.4 + - - +
166D SER* 3.3 12.7 + - - +
168D MET* 1.3 74.5 - - - +
170D PHE* 1.3 62.1 + - - +
172D ASN* 3.1 22.5 + - - +
173D LEU* 3.2 28.0 + - - +
300D FAD 3.1 59.8 + - - -
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Residues in contact with PHE 170 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76D TRP* 3.6 48.7 - + - -
79D HIS* 3.6 33.2 - + + +
160D TRP* 3.7 24.0 - + + -
166D SER 2.9 13.0 + - - +
167D LEU* 3.4 12.1 - - + +
169D ASN* 1.3 76.5 - - - +
171D LEU* 1.3 62.4 + - + +
173D LEU 3.3 0.7 + - - -
174D ARG* 2.8 64.5 + - + +
183D ILE* 4.5 5.4 - - + -
187D ALA* 4.0 19.1 - - + -
190D ILE* 4.0 21.3 - - + -
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Residues in contact with LEU 171 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167D LEU* 3.0 24.9 + - + +
168D MET* 3.9 3.8 - - - +
169D ASN 3.3 0.2 - - - -
170D PHE* 1.3 75.5 - - + +
172D ASN* 1.3 66.4 + - - +
175D ALA* 3.1 37.3 + - + +
187D ALA* 3.1 39.3 - - + +
190D ILE* 4.0 10.3 - - + -
191D ALA* 3.9 29.8 - - + +
194D PHE* 4.2 21.5 - - + -
202D PHE* 4.8 1.3 - - + -
205D PHE* 4.2 20.9 - - + -
210D TYR* 3.5 5.3 - - - -
215D LEU* 4.2 4.3 - - + -
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Residues in contact with ASN 172 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168D MET* 2.9 20.8 + - - +
169D ASN* 3.1 16.3 + - - +
171D LEU* 1.3 77.2 - - - +
173D LEU* 1.3 62.5 + - + +
176D ASP* 3.8 15.2 - - - +
205D PHE* 3.4 7.1 - - - -
209D ALA* 4.0 11.3 + - - +
210D TYR* 3.3 13.4 - - - -
211D LYS* 2.8 43.7 + - + +
212D GLY* 3.8 12.5 + - - +
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Residues in contact with LEU 173 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52B GLY 5.4 7.9 - - - +
79D HIS* 3.8 5.6 - - + -
169D ASN* 3.2 35.6 + - - +
170D PHE 4.0 2.7 - - - +
172D ASN* 1.3 81.5 - - + +
174D ARG* 1.3 67.2 + - - +
176D ASP* 4.0 9.1 - - - +
179D ALA* 3.5 8.7 + - - +
300D FAD 3.0 74.9 - - + +
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Residues in contact with ARG 174 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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303A UMP 2.9 46.9 + - - -
75D GLN* 3.1 30.8 + - - +
79D HIS* 3.0 23.2 + - - +
170D PHE* 2.8 47.6 + - + +
173D LEU* 1.3 78.5 - - - +
175D ALA* 1.3 55.1 + - - +
176D ASP 3.0 10.8 + - - -
179D ALA* 3.6 12.2 - - - +
183D ILE* 4.0 23.5 - - + +
184D GLN* 3.4 21.8 - - - -
187D ALA* 3.6 16.8 - - + -
300D FAD 3.5 33.7 + - - +
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Residues in contact with ALA 175 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171D LEU* 3.1 25.3 + - + +
174D ARG* 1.3 72.7 - - - +
176D ASP* 1.3 61.1 + - - +
187D ALA* 3.5 18.2 - - + +
210D TYR* 2.4 31.0 + - - -
212D GLY* 3.7 0.2 - - - -
214D ILE* 3.6 16.4 - - + +
215D LEU* 3.7 33.4 - - + -
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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