Contacts of the helix formed by residues 179 - 188 (chain C) in PDB entry 3E6C
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 SER 179 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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538A T 4.4 6.5 - - - -
539A G 3.4 15.9 - - - -
178C LEU* 1.3 75.5 - - - +
180C GLN* 1.3 64.6 + - - +
181C LYS* 3.8 8.2 + - - +
182C SER* 3.1 29.2 + - - -
183C ILE* 3.0 25.3 + - - +
209C LYS* 4.0 4.0 - - - +
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Residues in contact with GLN 180 (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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539A G 3.0 40.1 + - - +
540A T 3.1 20.3 + - - -
178C LEU 3.9 0.4 + - - -
179C SER* 1.3 68.1 - - - +
181C LYS* 1.3 59.9 + - - +
183C ILE* 3.6 5.9 - - - +
184C GLY* 2.9 26.0 + - - -
191C HIS* 4.3 8.0 + - + +
194C VAL* 3.7 17.9 - - + +
195C SER* 3.4 33.6 - - - +
198C LEU* 3.5 34.0 - - + +
209C LYS* 4.3 9.6 - - + +
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Residues in contact with LYS 181 (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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538A T 3.3 43.8 + - + +
539A G 3.0 18.1 + - - +
62C LYS* 5.0 10.9 - - - +
77C TYR* 5.3 1.8 + - - -
179C SER* 3.2 7.8 - - - +
180C GLN* 1.3 75.1 - - - +
182C SER* 1.3 57.2 + - - +
184C GLY* 3.3 3.5 + - - -
185C GLU* 2.9 57.8 + - + +
191C HIS* 4.6 15.9 - - + +
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Residues in contact with SER 182 (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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74C LEU* 5.7 0.2 - - - -
77C TYR* 3.7 25.6 + - - -
178C LEU* 4.2 15.5 - - - -
179C SER* 3.1 22.9 + - - -
181C LYS* 1.3 75.5 - - - +
183C ILE* 1.3 58.0 + - - +
185C GLU* 3.0 12.3 + - - +
186C ILE* 2.8 44.3 + - - +
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Residues in contact with ILE 183 (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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153C ILE* 4.7 14.4 - - + -
156C LEU* 4.5 11.4 - - + -
157C PHE* 3.7 29.6 - - + -
178C LEU* 3.7 24.7 - - + -
179C SER 3.0 19.0 + - - +
180C GLN* 3.6 13.0 - - - +
182C SER* 1.3 75.2 - - - +
184C GLY* 1.3 63.1 + - - +
186C ILE* 3.3 7.1 + - - +
187C THR* 2.9 42.1 + - + +
194C VAL* 4.0 16.4 - - + -
198C LEU* 4.5 5.4 - - + -
209C LYS* 4.3 19.7 - - + -
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Residues in contact with GLY 184 (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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180C GLN 2.9 13.6 + - - -
181C LYS* 3.3 4.9 + - - -
183C ILE* 1.3 76.5 - - - +
185C GLU* 1.3 57.2 + - - +
187C THR* 3.9 2.5 - - - -
188C GLY* 2.8 25.8 + - - -
189C VAL 3.0 28.7 + - - +
191C HIS* 5.1 2.7 - - - -
194C VAL* 3.7 13.4 - - - +
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Residues in contact with GLU 185 (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 LYS* 4.8 7.3 + - - -
74C LEU* 3.9 36.1 - - + +
77C TYR* 3.8 18.2 + - - -
181C LYS* 2.9 51.1 + - + +
182C SER* 3.0 15.3 + - - +
184C GLY* 1.3 78.1 - - - +
186C ILE* 1.3 62.5 + - - +
188C GLY* 3.7 5.9 + - - -
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Residues in contact with ILE 186 (chain C).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14C ILE 5.2 0.4 - - - +
15C ILE* 4.4 16.8 - - + -
16C PRO* 3.8 40.6 - - + -
17C ASP* 6.4 0.2 - - + -
74C LEU* 4.3 11.4 - - + -
77C TYR* 5.7 4.7 - - + -
136C TYR* 3.9 9.8 + - - +
140C GLN* 3.4 18.5 + - - +
156C LEU* 4.5 15.0 - - + -
178C LEU* 4.3 19.5 - - + -
182C SER* 2.8 27.1 + - - +
183C ILE* 3.8 4.5 - - - +
185C GLU* 1.3 79.6 - - - +
187C THR* 1.3 66.4 + - + +
188C GLY 3.7 0.2 + - - -
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Residues in contact with THR 187 (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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140C GLN* 4.3 8.9 + - - +
144C MET* 4.7 2.7 - - - +
152C ARG* 3.1 47.4 + - + +
153C ILE* 4.0 9.6 - - - +
156C LEU* 3.8 29.2 - - + -
183C ILE* 2.9 31.2 + - + +
184C GLY* 3.7 0.3 + - - -
186C ILE* 1.3 79.5 - - + +
188C GLY* 1.3 61.3 + - - +
189C VAL* 3.1 26.4 - - - +
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Residues in contact with GLY 188 (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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503B A 4.4 5.5 + - - -
144C MET* 4.9 10.4 - - - +
149C PRO* 4.7 0.5 - - - +
152C ARG* 3.5 14.8 + - - -
184C GLY 2.8 11.6 + - - -
185C GLU 3.7 5.7 + - - -
186C ILE 3.4 3.0 + - - -
187C THR* 1.3 79.5 - - - +
189C VAL* 1.3 55.8 + - - +
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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