Contacts of the helix formed by residues 184 - 195 (chain C) in PDB entry 3AP3
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 ASP 184 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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183C ARG* 1.3 74.2 - - + +
185C GLY* 1.3 59.0 + - - +
186C ARG* 3.2 40.4 + - - +
187C ALA* 2.9 27.9 + - + +
188C SER* 3.2 8.0 + - - -
239C GLU* 3.4 8.3 + - - +
301C TRP* 4.4 0.6 - - - -
320C LEU* 2.9 25.8 - - - +
325C TYR* 3.5 33.2 + - + -
332C PRO* 4.1 0.3 - - - +
334C TYR* 3.1 28.8 + - - +
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Residues in contact with GLY 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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183C ARG 2.9 4.8 + - - -
184C ASP* 1.3 73.9 + - - +
186C ARG* 1.3 52.3 + - - +
188C SER* 3.6 1.7 - - - -
189C VAL* 2.7 40.2 + - - +
211C LEU* 3.9 7.2 - - - -
214C TRP* 3.1 46.3 - - - -
320C LEU* 3.6 2.9 - - - +
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Residues in contact with ARG 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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184C ASP* 3.1 29.7 + - - +
185C GLY* 1.3 76.9 - - - +
187C ALA* 1.3 56.5 + - - +
189C VAL* 4.3 1.5 - - - +
190C HIS* 3.1 28.6 + - - +
211C LEU* 4.0 13.2 - - + +
301C TRP* 3.3 47.7 - - + +
305C ILE* 4.7 7.4 - - + +
313C MET* 3.6 35.1 - - + +
320C LEU* 4.0 9.6 - - + +
325C TYR* 4.9 1.2 - - - +
326C ASP 2.8 23.5 + - - +
327C PRO* 3.0 30.8 + - - +
329C ALA 3.1 12.5 + - - -
330C ASN* 3.8 6.1 - - - +
332C PRO* 3.3 15.2 - - - +
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Residues in contact with ALA 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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1C A3P 4.0 0.5 + - - -
183C ARG* 3.6 33.4 + - + +
184C ASP* 2.9 13.7 + - + +
186C ARG* 1.3 76.3 - - - +
188C SER* 1.3 60.0 + - - +
190C HIS* 4.1 2.5 - - - +
191C SER* 3.0 28.3 + - - -
297C ALA 4.9 0.9 - - - +
298C LEU 4.2 7.6 - - - +
301C TRP* 3.9 30.9 - - + +
334C TYR* 5.2 0.4 - - - +
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Residues in contact with SER 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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77C PRO 4.1 9.4 - - - -
78C ARG* 2.9 28.8 + - - +
79C SER* 3.3 16.3 + - - -
183C ARG* 3.9 11.8 + - - +
184C ASP 3.2 6.5 + - - -
185C GLY* 3.3 11.2 + - - -
187C ALA* 1.3 76.2 - - - +
189C VAL* 1.3 58.9 + - - +
191C SER* 3.2 2.9 + - - -
192C MET* 2.8 36.6 + - - +
214C TRP* 4.2 11.8 + - - -
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Residues in contact with VAL 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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185C GLY 2.7 22.1 + - - +
186C ARG 4.3 1.3 - - - +
188C SER* 1.3 69.4 - - - +
190C HIS* 1.3 66.0 + - - +
192C MET* 3.2 14.9 - - + +
193C ILE* 3.0 34.2 + - + +
207C TYR* 3.8 16.2 - - + -
210C CYS* 3.2 50.5 - - + +
211C LEU* 3.7 22.4 - - + -
214C TRP* 4.0 9.4 - - + -
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Residues in contact with HIS 190 (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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112A ALA* 4.4 9.4 + - + +
186C ARG 3.1 20.5 + - - +
187C ALA 4.1 4.0 - - - +
189C VAL* 1.3 77.7 - - - +
191C SER* 1.3 66.5 + - - +
192C MET 3.3 0.2 + - - -
193C ILE* 3.9 0.3 - - - -
194C THR* 2.9 51.6 + - + +
207C TYR* 3.3 33.8 + - + +
300C LYS* 4.0 26.2 + - + +
301C TRP* 3.5 41.2 + - + -
304C HIS* 4.1 22.5 - + + +
305C ILE* 5.0 0.9 - - + -
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Residues in contact with SER 191 (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 A3P 2.4 37.6 + - - -
78C ARG* 3.3 24.0 + - - +
183C ARG* 4.0 1.1 - - - -
187C ALA 3.0 22.9 + - - -
188C SER 3.2 5.6 + - - -
190C HIS* 1.3 79.2 - - - +
192C MET* 1.3 56.3 + - - +
194C THR* 3.4 5.1 + - - -
195C ARG* 3.0 36.7 + - - +
300C LYS* 5.9 0.9 - - - +
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Residues in contact with MET 192 (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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76C VAL* 4.1 17.5 - - + -
77C PRO 4.0 18.2 - - - +
78C ARG* 3.8 11.0 - - + -
188C SER* 2.8 28.1 + - - +
189C VAL* 3.2 28.9 - - + +
191C SER* 1.3 70.9 + - - +
193C ILE* 1.3 62.5 + - - +
195C ARG 4.2 0.2 - - - -
196C LYS* 3.6 1.4 + - - -
197C VAL* 3.2 49.6 + - + +
199C ILE* 4.5 19.1 - - + -
210C CYS* 4.5 20.2 - - - +
214C TRP* 5.4 2.2 - - + -
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Residues in contact with ILE 193 (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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113A TRP* 6.1 0.2 - - - +
105B ARG* 3.1 42.7 + - - +
189C VAL* 3.0 27.7 + - + +
190C HIS 3.9 2.0 - - - +
192C MET* 1.3 77.4 - - - +
194C THR* 1.3 66.7 + - + +
196C LYS* 3.6 5.0 + - - -
206C SER 3.8 23.1 - - - +
207C TYR* 3.4 54.1 - - + +
210C CYS* 3.8 16.2 - - - -
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Residues in contact with THR 194 (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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112A ALA* 3.9 30.1 + - + -
113A TRP* 4.0 27.1 - - + +
190C HIS* 2.9 51.0 + - + +
191C SER* 3.4 8.0 + - - -
193C ILE* 1.3 78.2 - - + +
195C ARG* 1.3 64.6 + - - +
196C LYS* 3.3 17.2 - - - +
207C TYR* 4.2 7.6 - - - +
300C LYS* 5.9 1.7 - - - -
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Residues in contact with ARG 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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1C A3P 2.4 44.3 + - - -
78C ARG* 3.5 16.6 - - - +
191C SER* 3.0 20.4 + - - +
194C THR* 1.3 80.5 + - - +
196C LYS* 1.3 56.2 + - - +
197C VAL* 3.5 10.6 + - + +
284C ARG* 2.8 41.8 + - + +
287C ASP* 5.9 0.4 + - - -
288C GLN* 3.2 38.7 + - - +
300C LYS* 3.6 15.0 - - - +
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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