Contacts of the helix formed by residues 194 - 212 (chain C) in PDB entry 5HP1
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 GLU 194 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104C LYS* 5.1 7.0 - - - -
192C ASP 4.2 0.2 + - - -
193C LEU* 1.3 70.3 - - - +
195C ILE* 1.3 63.4 + - + +
196C GLY* 2.7 51.0 + - - -
197C GLN* 2.9 38.4 + - - +
198C HIS 3.1 8.3 + - - -
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Residues in contact with ILE 195 (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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104C LYS* 5.5 1.8 - - + +
105C SER* 3.3 29.5 + - - +
106C VAL 5.5 0.7 - - - +
193C LEU 3.4 3.0 + - - -
194C GLU* 1.3 79.1 - - + +
196C GLY* 1.3 60.0 + - - +
198C HIS* 3.7 7.6 - - + -
199C ARG* 3.0 71.9 + - + +
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Residues in contact with GLY 196 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194C GLU* 2.7 27.1 + - - -
195C ILE* 1.3 71.2 - - - +
197C GLN* 1.3 64.8 + - - -
198C HIS 3.0 1.9 + - - -
199C ARG* 3.1 15.1 + - - +
200C THR* 3.2 15.3 + - - -
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Residues in contact with GLN 197 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193C LEU* 3.6 34.8 - - + +
194C GLU* 2.9 30.0 + - - +
196C GLY* 1.3 70.5 - - - -
198C HIS* 1.3 60.0 + - - +
200C THR* 3.5 9.1 - - - -
201C LYS* 3.0 32.5 + - + +
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Residues in contact with HIS 198 (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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105C SER* 3.5 33.2 - - - +
106C VAL 3.7 5.5 - - - -
107C THR* 2.4 29.7 + - - -
178C ILE* 6.0 0.8 - - + +
189C VAL* 3.8 15.7 - - + -
190C GLY 4.7 0.2 - - - -
191C SER* 2.8 30.5 + - - +
193C LEU* 4.4 4.8 - - + +
194C GLU 3.1 10.7 + - - +
195C ILE* 3.7 24.0 - - + +
196C GLY 3.0 0.6 - - - -
197C GLN* 1.3 74.4 - - - +
199C ARG* 1.3 74.7 + - - +
200C THR 3.1 0.2 + - - -
201C LYS* 3.3 6.6 + - - +
202C ILE* 3.1 38.8 + - + +
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Residues in contact with ARG 199 (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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106C VAL 4.1 10.7 + - - -
107C THR* 4.1 15.4 + - - +
195C ILE* 3.0 54.2 + - + +
196C GLY* 3.1 5.6 + - - +
198C HIS* 1.3 83.4 - - - +
200C THR* 1.3 63.0 + - - +
202C ILE* 3.5 9.8 - - - +
203C GLU* 3.2 26.5 + - - +
221C HIS* 4.3 2.8 - - - -
223C LYS* 3.1 70.2 + - - +
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Residues in contact with THR 200 (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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196C GLY 3.2 12.3 + - - -
197C GLN* 3.5 13.9 - - + +
198C HIS 3.1 0.8 - - - -
199C ARG* 1.3 73.3 - - - +
201C LYS* 1.3 60.6 + - + +
203C GLU* 2.8 30.1 + - + +
204C GLU* 3.0 29.1 + - + +
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Residues in contact with LYS 201 (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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171C PHE* 3.8 7.3 - - + -
175C ASN* 4.0 20.5 + - - +
177C ASP* 6.1 1.0 - - - +
178C ILE* 4.2 29.5 - - + +
193C LEU* 4.3 15.6 - - + +
197C GLN* 3.0 22.0 + - - +
198C HIS* 3.7 6.5 - - - +
200C THR* 1.3 79.6 - - + +
202C ILE* 1.3 66.3 + - + +
204C GLU* 3.0 35.8 + - - +
205C LEU* 3.0 20.3 + - - +
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Residues in contact with ILE 202 (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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107C THR* 3.3 28.9 - - + +
109C LEU* 3.6 16.8 - - + -
178C ILE* 6.4 0.2 - - + -
189C VAL* 3.7 34.1 - - + -
198C HIS* 3.1 26.7 + - + +
199C ARG* 3.5 11.7 - - - +
201C LYS* 1.3 77.7 - - + +
203C GLU* 1.3 58.5 + - - +
205C LEU* 2.8 25.0 + - + +
206C ARG* 3.0 19.0 + - - +
221C HIS* 3.6 30.7 - - + +
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Residues in contact with GLU 203 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199C ARG* 3.2 15.0 + - + +
200C THR* 2.8 17.2 + - + +
202C ILE* 1.3 73.7 - - - +
204C GLU* 1.3 60.7 + - - +
206C ARG* 3.4 35.8 + - - +
207C GLN* 3.0 45.3 + - + +
221C HIS* 4.3 8.1 + - - -
223C LYS* 5.6 5.4 + - - -
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Residues in contact with GLU 204 (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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171C PHE* 3.9 13.3 - - + -
175C ASN* 4.3 6.6 + - - +
200C THR* 3.0 27.2 + - + +
201C LYS* 3.3 39.8 - - - +
203C GLU* 1.3 78.4 - - + +
205C LEU* 1.3 61.5 + - - +
207C GLN* 3.5 7.0 + - - +
208C HIS* 3.1 24.8 + - - +
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Residues in contact with LEU 205 (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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109C LEU* 4.4 14.4 - - + -
168C LEU* 4.2 20.2 - - + -
171C PHE* 3.6 43.9 - - + -
180C ILE* 4.5 7.0 - - + -
187C LEU* 4.2 14.1 - - + -
189C VAL* 3.9 30.1 - - + -
201C LYS 3.0 7.0 + - - +
202C ILE* 2.8 14.7 + - + +
204C GLU* 1.3 75.3 - - - +
206C ARG* 1.3 60.4 + - + +
208C HIS* 3.5 3.2 + - + +
209C LEU* 2.9 46.1 + - + +
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Residues in contact with ARG 206 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109C LEU* 4.4 11.4 - - + +
202C ILE* 3.0 13.6 + - - +
203C GLU* 3.4 38.9 + - - +
205C LEU* 1.3 75.8 - - + +
207C GLN* 1.3 59.8 + - - +
209C LEU* 3.2 8.9 + - - +
210C LEU* 2.7 36.0 + - - +
214C LEU 4.4 0.9 - - - +
216C THR* 2.3 58.1 + - + +
217C PRO 3.9 2.8 + - - -
218C ASP* 3.4 24.7 + - - -
221C HIS* 3.2 30.7 - - - -
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Residues in contact with GLN 207 (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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203C GLU* 3.0 35.8 + - + +
204C GLU* 3.7 7.0 - - - +
205C LEU 3.2 0.2 - - - -
206C ARG* 1.3 78.2 - - - +
208C HIS* 1.3 57.2 + - - +
210C LEU* 2.8 20.1 + - - +
211C ARG* 2.7 35.8 + - - +
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Residues in contact with HIS 208 (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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167C ILE* 2.9 41.2 + - + +
168C LEU* 5.3 0.9 - - - -
170C PRO* 4.0 18.8 - - + -
171C PHE* 4.2 31.5 - + + +
204C GLU 3.1 15.0 + - - +
205C LEU* 3.6 7.0 - - + +
207C GLN* 1.3 76.4 - - - +
209C LEU* 1.3 69.5 + - + +
211C ARG* 3.1 19.5 - - - +
212C TRP* 3.1 39.3 + + - -
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Residues in contact with LEU 209 (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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109C LEU* 5.6 1.3 - - + -
111C VAL* 4.3 13.5 - - + -
164C MET* 4.4 8.3 - - + -
167C ILE* 3.9 24.5 - - + -
168C LEU* 4.7 7.9 - - + -
187C LEU* 4.3 13.0 - - + -
205C LEU* 2.9 38.0 + - + +
206C ARG* 3.5 6.3 - - - +
208C HIS* 1.3 79.2 - - + +
210C LEU* 1.3 63.4 + - - +
212C TRP* 3.1 10.0 + - - +
214C LEU* 2.9 50.3 + - + +
216C THR* 4.0 23.6 - - + -
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Residues in contact with LEU 210 (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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2C ILE* 4.0 9.9 - - - +
206C ARG 2.7 20.7 + - - +
207C GLN* 3.4 20.4 - - - +
209C LEU* 1.3 70.4 - - - +
211C ARG* 1.3 60.5 + - - +
213C GLY* 2.9 20.2 + - - -
214C LEU 3.3 14.5 + - - +
215C THR* 3.9 26.5 - - + -
216C THR 5.4 0.9 - - - +
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Residues in contact with ARG 211 (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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1C PRO 5.2 2.6 + - - -
2C ILE* 3.4 12.4 - - - +
3C SER* 2.5 67.1 + - - +
207C GLN 2.7 15.5 + - - +
208C HIS* 3.1 22.4 + - - +
210C LEU* 1.3 73.3 - - - +
212C TRP* 1.3 104.3 + - + +
213C GLY 3.4 0.2 - - - -
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Residues in contact with TRP 212 (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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2C ILE* 4.6 3.9 - - - +
3C SER* 3.3 28.3 - - - +
4C PRO* 4.3 10.7 - - - +
5C ILE* 3.9 33.5 + - + +
6C GLU* 5.6 5.4 - - + -
117C SER 4.4 2.4 - - - +
166C LYS 5.8 0.9 - - - -
167C ILE* 3.7 51.5 - - + +
170C PRO* 6.1 3.1 - - + -
208C HIS* 3.1 41.1 + + - -
209C LEU 3.1 8.9 + - - +
211C ARG* 1.3 119.5 - - + +
213C GLY* 1.3 62.0 + - - +
214C LEU* 3.3 3.9 + - + +
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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
------------------------------------------------------------
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