Contacts of the helix formed by residues 184 - 196 (chain A) in PDB entry 3AP1
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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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183A ARG* 1.3 69.1 - - - +
185A GLY* 1.3 64.6 + - - +
186A ARG* 2.8 58.5 + - - +
187A ALA* 2.9 21.1 + - + +
188A SER* 3.2 9.2 + - - -
239A GLU* 3.0 16.9 + - - +
301A TRP* 3.8 1.7 - - - -
320A LEU* 3.5 4.3 - - - +
325A TYR* 3.2 28.5 - - + -
332A PRO* 3.8 0.3 - - - +
334A TYR* 2.6 31.9 + - - +
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Residues in contact with GLY 185 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183A ARG 3.0 4.0 + - - -
184A ASP* 1.3 74.5 + - - +
186A ARG* 1.3 56.7 + - - +
188A SER* 3.8 1.2 - - - -
189A VAL* 2.8 35.3 + - - +
211A LEU* 3.7 6.5 - - - -
214A TRP* 3.2 46.3 - - - -
320A LEU* 3.5 5.4 - - - +
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Residues in contact with ARG 186 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184A ASP* 2.8 38.1 + - - +
185A GLY* 1.3 78.1 - - - +
187A ALA* 1.3 56.2 + - - +
189A VAL* 4.2 0.8 - - - +
190A HIS* 3.0 30.8 + - - +
211A LEU* 3.8 9.6 - - + +
301A TRP* 3.5 41.4 - - + +
305A ILE* 4.0 11.2 - - + +
313A MET* 3.7 38.6 - - + +
320A LEU* 4.0 11.0 - - + +
325A TYR* 4.2 6.9 - - - +
326A ASP 3.1 19.9 + - - -
327A PRO* 3.3 22.6 + - - +
329A ALA 2.9 20.6 + - - -
330A ASN* 4.6 3.9 - - - +
332A PRO* 3.5 13.9 - - - +
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Residues in contact with ALA 187 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1A A3P 4.5 0.7 + - - -
183A ARG* 3.4 35.4 + - + +
184A ASP* 2.9 16.2 + - + +
186A ARG* 1.3 75.9 - - - +
188A SER* 1.3 57.7 + - - +
190A HIS* 3.5 2.9 + - - +
191A SER* 2.9 28.9 + - - -
239A GLU* 5.0 0.4 - - - +
297A ALA 5.0 0.4 - - - +
298A LEU 4.3 5.6 - - - +
301A TRP* 3.5 30.9 - - + +
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Residues in contact with SER 188 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77A PRO 4.0 12.3 - - - -
78A ARG* 3.1 31.9 + - - +
79A SER* 3.3 13.4 + - - -
183A ARG* 3.7 9.7 + - - +
184A ASP 3.2 11.3 + - - -
185A GLY 3.8 5.4 - - - -
187A ALA* 1.3 76.7 - - - +
189A VAL* 1.3 58.8 + - - +
191A SER* 3.3 3.1 - - - -
192A MET* 3.0 29.7 + - - +
214A TRP* 4.1 16.4 + - - -
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Residues in contact with VAL 189 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185A GLY 2.8 20.8 + - - +
186A ARG 4.2 2.0 - - - +
188A SER* 1.3 76.0 - - - +
190A HIS* 1.3 67.9 + - - +
192A MET* 3.2 11.2 + - + +
193A ILE* 3.0 24.7 + - + +
207A TYR* 3.7 25.1 - - + +
210A CYS* 3.6 48.2 - - + +
211A LEU* 3.7 21.8 - - + +
214A TRP* 3.8 11.7 - - + -
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Residues in contact with HIS 190 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1A A3P 5.8 0.4 - - - -
186A ARG 3.0 20.3 + - - +
187A ALA 3.8 2.9 - - - +
189A VAL* 1.3 76.6 - - - +
191A SER* 1.3 58.5 + - - +
193A ILE* 4.0 0.3 - - - +
194A THR* 2.9 63.1 + - + +
207A TYR* 3.0 32.1 + - + -
300A LYS* 4.2 22.8 + - + +
301A TRP* 3.5 31.9 + - + -
304A HIS* 3.6 32.0 - + + +
305A ILE* 5.0 0.9 - - + -
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Residues in contact with SER 191 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1A A3P 2.6 36.1 + - - -
78A ARG* 2.7 31.4 + - - +
183A ARG* 4.2 1.6 - - - -
187A ALA 2.9 15.7 + - - -
188A SER* 3.3 9.9 - - - -
190A HIS* 1.3 79.8 - - - +
192A MET* 1.3 63.3 + - - +
194A THR* 4.1 4.3 - - - -
195A ARG* 3.0 29.4 + - - +
300A LYS* 6.3 0.2 - - - +
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Residues in contact with MET 192 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76A VAL* 4.5 8.5 - - + -
77A PRO 4.2 13.2 - - - +
78A ARG* 3.9 12.5 - - + +
188A SER* 3.0 26.7 + - - +
189A VAL* 3.3 17.7 - - + +
191A SER* 1.3 76.0 + - - +
193A ILE* 1.3 63.3 + - + +
196A LYS* 2.9 24.3 + - - -
197A VAL* 3.0 30.3 + - + +
199A ILE* 3.6 22.4 - - + -
202A PHE* 3.6 34.3 - - + -
204A LEU* 3.9 12.9 - - + +
210A CYS* 4.1 13.2 - - - -
214A TRP* 5.4 0.7 - - + -
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Residues in contact with ILE 193 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189A VAL* 3.0 26.3 + - + +
190A HIS 4.1 2.0 - - - +
192A MET* 1.3 78.5 - - + +
194A THR* 1.3 66.6 - - + +
196A LYS* 3.3 20.1 + - - +
204A LEU* 3.5 32.1 - - + +
206A SER 3.9 4.9 - - - +
207A TYR* 3.6 66.6 - - + +
210A CYS* 4.1 13.9 - - - -
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Residues in contact with THR 194 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190A HIS* 2.9 61.6 + - + +
191A SER* 3.6 4.9 + - - -
193A ILE* 1.3 78.4 - - + +
195A ARG* 1.3 65.7 + - - +
196A LYS* 3.7 8.5 + - - +
207A TYR* 3.9 7.9 - - - +
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Residues in contact with ARG 195 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A A3P 2.8 37.9 + - - -
78A ARG* 3.4 21.0 - - - +
191A SER* 3.0 18.8 + - - +
194A THR* 1.3 82.2 - - - +
196A LYS* 1.3 65.3 + - - +
197A VAL* 4.1 10.5 - - + -
284A ARG* 2.8 36.6 + - - +
287A ASP* 4.2 8.7 + - - -
288A GLN* 3.6 30.4 + - - +
300A LYS* 3.8 11.1 - - - +
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Residues in contact with LYS 196 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192A MET 2.9 11.7 + - - -
193A ILE 3.3 13.7 + - - +
194A THR 4.2 6.6 + - - +
195A ARG* 1.3 80.3 - - - +
197A VAL* 1.3 60.9 + - - +
198A THR* 3.6 10.4 + - + +
204A LEU* 4.0 18.8 - - + -
284A ARG* 2.9 13.7 + - - -
1005S ASP* 3.9 0.9 - - - +
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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
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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