Contacts of the helix formed by residues 180 - 189 (chain C) in PDB entry 4QY2
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 180 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178C PRO* 3.4 2.0 - - - +
179C SER* 1.3 84.4 + - - +
181C THR* 1.3 63.0 + - - +
182C GLN* 3.3 7.8 + - - +
183C GLU* 2.7 31.4 + - - +
184C LYS 3.1 17.5 + - - -
210C VAL* 3.4 19.3 - - - +
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Residues in contact with THR 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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180C SER* 1.3 71.0 - - - +
182C GLN* 1.3 61.9 + - - +
184C LYS* 3.5 4.5 + - + +
185C ASN* 3.0 50.5 + - - +
210C VAL* 3.6 18.2 - - + +
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Residues in contact with GLN 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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180C SER* 3.2 6.8 + - - +
181C THR* 1.3 76.9 - - - +
183C GLU* 1.3 67.1 + - - +
185C ASN* 3.3 11.1 + - - +
186C ASP* 3.0 60.2 + - - +
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Residues in contact with GLU 183 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88C TYR* 3.9 8.5 + - - -
144C TRP* 5.1 1.7 - - - -
176C HIS* 3.5 21.1 + - - -
178C PRO* 4.0 8.0 - - + +
179C SER* 2.8 38.8 + - - -
180C SER* 2.7 23.6 + - - +
182C GLN* 1.3 73.2 - - - +
184C LYS* 1.3 65.0 + - - +
186C ASP* 3.5 6.1 + - - +
187C LEU* 3.2 40.0 + - + +
219C GLN* 5.7 0.5 - - - +
221C GLY* 4.8 2.4 + - - -
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Residues in contact with LYS 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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178C PRO* 4.0 23.9 - - + +
180C SER 3.1 11.9 + - - +
181C THR* 3.5 10.8 - - + +
183C GLU* 1.3 77.3 - - - +
185C ASN* 1.3 74.4 + - - +
187C LEU 3.1 2.9 + - - -
188C TYR* 3.0 35.1 + - + -
189C GLY 3.1 28.0 + - - -
190C THR 3.7 6.9 + - - -
191C GLN 3.0 27.3 + - - -
193C ILE* 3.9 18.9 - - + +
208C PRO* 5.7 7.2 - - + +
210C VAL* 3.9 17.3 - - + -
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Residues in contact with ASN 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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151C GLY* 3.3 11.7 - - - -
181C THR* 3.0 37.8 + - - +
182C GLN* 3.9 11.8 - - - +
184C LYS* 1.3 88.4 + - - +
186C ASP* 1.3 63.8 + - - +
189C GLY* 2.9 45.1 + - - +
190C THR* 3.5 25.0 - - + +
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Residues in contact with ASP 186 (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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146C VAL* 5.3 0.7 - - - +
147C SER* 4.9 3.1 - - - +
150C LYS* 3.7 42.5 + - + +
151C GLY* 3.1 25.8 + - - +
182C GLN* 3.0 47.5 + - - +
183C GLU* 3.7 6.9 + - - +
185C ASN* 1.3 75.5 - - - +
187C LEU* 1.3 67.0 + - + +
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Residues in contact with LEU 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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144C TRP* 3.9 21.5 - - + -
146C VAL* 3.7 24.1 - - + -
147C SER* 3.0 31.7 + - - -
176C HIS* 4.0 10.8 - - + -
183C GLU* 3.2 27.3 + - + +
184C LYS* 3.1 2.2 + - - -
186C ASP* 1.3 83.4 - - + +
188C TYR* 1.3 98.8 + - + +
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Residues in contact with TYR 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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144C TRP* 3.0 17.0 + - - -
145C LEU 3.5 21.5 - - - -
146C VAL* 4.0 2.0 - - + -
147C SER* 4.2 0.4 - - - -
152C GLN 3.7 6.3 - - - -
153C ASN* 3.4 1.9 - - - -
154C PHE* 2.9 30.7 + + + +
176C HIS* 2.8 38.1 + - + +
178C PRO* 4.2 11.9 - - + -
184C LYS* 3.0 19.0 + - + +
187C LEU* 1.3 101.7 - - + +
189C GLY* 1.3 62.0 + - - +
191C GLN* 3.8 9.4 + - - +
193C ILE* 3.5 29.4 - - + -
208C PRO* 5.8 1.8 - - + -
242C GLY* 3.6 14.8 - - - -
243C GLY* 3.4 29.0 - - - -
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Residues in contact with GLY 189 (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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151C GLY 3.6 13.7 - - - -
152C GLN 3.6 6.2 + - - -
153C ASN* 3.2 10.1 - - - -
184C LYS* 3.1 25.8 - - - -
185C ASN* 2.9 26.1 + - - +
187C LEU 3.9 0.2 - - - -
188C TYR* 1.3 79.9 - - - +
190C THR* 1.3 60.3 + - - -
191C GLN* 3.5 1.8 - - - -
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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