Contacts of the helix formed by residues 182 - 196 (chain A) in PDB entry 4KPF
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 ASN 182 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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95A ARG* 3.5 6.9 - - - +
181A HIS* 1.3 72.4 - - - +
183A LEU* 1.3 67.3 + - - +
184A ALA* 3.1 30.0 + - - +
185A GLU* 3.0 38.2 + - - +
186A VAL* 3.0 24.2 + - - +
212A ASP* 3.1 31.7 + - + +
476A THR 2.8 25.1 + - - +
477A PRO* 3.5 13.5 + - - +
478A ARG* 3.6 4.1 - - - +
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Residues in contact with LEU 183 (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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95A ARG* 5.4 1.6 - - - +
96A GLU* 4.1 19.7 + - - +
126A ILE* 4.9 4.0 - - + -
159A PHE* 3.9 29.2 - - + -
164A VAL* 3.6 31.5 - - + +
181A HIS 3.3 5.1 + - - -
182A ASN* 1.3 72.3 - - - +
184A ALA* 1.3 65.5 + - - +
186A VAL* 3.4 1.7 + - - +
187A ILE* 3.0 49.9 + - + +
470A VAL* 4.2 9.6 - - + +
471A LYS* 4.0 18.2 - - - -
474A PHE* 4.2 26.0 - - + +
475A ALA* 4.4 2.5 - - - +
476A THR* 5.4 2.0 - - + +
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Residues in contact with ALA 184 (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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182A ASN* 3.1 12.5 + - - +
183A LEU* 1.3 81.1 - - - +
185A GLU* 1.3 59.9 + - + +
187A ILE* 3.4 1.6 + - - +
188A ASP* 2.9 38.1 + - - +
471A LYS* 3.9 30.9 - - + +
475A ALA* 4.0 19.4 - - + +
476A THR 4.9 1.8 - - - +
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Residues in contact with GLU 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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182A ASN* 3.0 29.5 + - + +
184A ALA* 1.3 77.1 - - + +
186A VAL* 1.3 64.0 + - - +
188A ASP* 3.2 8.2 + - - +
189A ALA* 3.0 21.1 + - - +
207A PHE 3.2 24.8 - - - +
208A LEU* 4.2 10.5 - - + +
209A PRO* 3.7 17.8 - - + +
210A GLY 3.9 6.1 - - - +
478A ARG* 2.4 49.3 + - - +
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Residues in contact with VAL 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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160A PRO* 3.3 33.4 - - + +
163A LEU* 3.9 34.8 - - + -
164A VAL* 4.5 7.4 - - + -
181A HIS* 3.6 26.7 - - + -
182A ASN 3.0 19.4 + - - +
183A LEU 3.8 3.8 - - - +
185A GLU* 1.3 76.6 - - - +
187A ILE* 1.3 63.5 + - - +
189A ALA* 3.1 5.1 + - - +
190A ALA* 2.9 21.0 + - - +
208A LEU* 4.4 11.9 - - + -
346A LEU* 4.4 6.4 - - + +
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Residues in contact with ILE 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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160A PRO* 4.0 20.4 - - + -
183A LEU* 3.0 34.1 + - + +
184A ALA 3.9 2.7 - - - +
186A VAL* 1.3 76.3 - - - +
188A ASP* 1.3 64.3 + - - +
190A ALA* 3.3 5.9 + - - +
191A VAL* 2.9 29.2 + - + +
467A LEU* 3.5 52.9 - - + +
468A ARG* 4.5 1.8 - - + +
470A VAL* 3.7 23.1 - - + -
471A LYS* 3.9 17.7 - - + +
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Residues in contact with ASP 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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184A ALA* 2.9 26.4 + - - +
185A GLU* 3.2 8.8 + - - +
187A ILE* 1.3 74.7 - - - +
189A ALA* 1.3 63.4 + - - +
191A VAL* 3.4 6.6 + - - +
192A TYR* 3.1 22.0 + - - +
207A PHE* 4.1 26.1 - - + +
471A LYS* 2.8 34.4 + - - +
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Residues in contact with ALA 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 GLU 3.0 11.8 + - - +
186A VAL* 3.1 8.9 + - - +
188A ASP* 1.3 77.2 - - - +
190A ALA* 1.3 62.9 + - - +
192A TYR* 3.0 6.6 + - - +
193A MET* 2.9 23.4 + - - +
204A LEU* 4.0 11.4 - - + +
207A PHE* 3.8 14.6 - - + +
208A LEU* 4.0 22.0 - - + -
346A LEU* 3.9 20.0 - - + -
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Residues in contact with ALA 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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160A PRO* 5.4 1.3 - - + -
186A VAL* 2.9 18.1 + - + +
187A ILE* 3.8 7.4 - - - +
189A ALA* 1.3 77.2 - - - +
191A VAL* 1.3 57.6 + - - +
193A MET* 3.3 6.5 + - - -
194A ILE* 2.9 35.7 + - - +
346A LEU* 4.3 18.1 - - + +
349A TYR* 4.7 14.8 - - + -
350A ILE* 3.5 9.2 - - + +
467A LEU* 4.6 14.1 - - + -
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Residues in contact with VAL 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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187A ILE* 2.9 23.5 + - + +
188A ASP* 3.8 7.4 - - - +
190A ALA* 1.3 76.2 - - - +
192A TYR* 1.3 62.0 + - - +
194A ILE* 3.3 15.9 + - - +
195A ASP* 3.4 19.6 + - - +
464A LYS* 4.1 15.9 - - + +
467A LEU* 4.2 25.8 - - + -
468A ARG* 3.6 40.2 - - + +
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Residues in contact with TYR 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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188A ASP 3.1 12.4 + - - +
189A ALA* 3.0 9.4 + - - +
191A VAL* 1.3 75.6 - - - +
193A MET* 1.3 60.8 + - - +
195A ASP* 3.2 4.7 + - + -
196A HIS* 2.8 71.8 + + + +
199A ALA* 3.7 25.4 - - + -
203A LYS* 3.3 46.4 + - + +
204A LEU* 4.1 7.2 - - + -
207A PHE* 3.5 33.0 - + + -
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Residues in contact with MET 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 ALA 2.9 15.5 + - - +
190A ALA* 3.7 6.7 - - - +
192A TYR* 1.3 78.1 - - - +
194A ILE* 1.3 67.1 + - - +
196A HIS 3.9 7.4 - - - +
197A PRO* 3.1 42.3 - - + +
199A ALA* 4.8 3.4 - - - +
204A LEU* 4.3 23.8 - - + -
343A VAL* 3.3 21.8 - - + +
346A LEU* 3.4 14.8 - - + +
347A SER* 3.0 46.2 - - - +
350A ILE* 4.0 10.2 - - + +
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Residues in contact with ILE 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 ALA 2.9 25.5 + - - +
191A VAL* 3.6 7.0 - - - +
192A TYR 3.1 0.6 - - - -
193A MET* 1.3 80.1 - - - +
195A ASP* 1.3 61.1 + - - +
196A HIS 3.5 0.2 + - - -
197A PRO* 3.9 8.3 - - - +
350A ILE* 3.2 20.2 - - + -
460A TYR* 3.7 33.9 - - + +
463A MET* 2.9 41.5 - - + -
464A LYS* 3.5 34.8 - - + -
467A LEU* 3.9 12.3 - - + -
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Residues in contact with ASP 195 (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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191A VAL* 3.4 14.9 + - - +
192A TYR* 3.2 9.2 + - - +
194A ILE* 1.3 81.1 - - - +
196A HIS* 1.3 80.7 + - + +
197A PRO* 3.6 5.7 - - - +
464A LYS* 3.2 36.8 + - - +
468A ARG* 4.9 3.1 + - - -
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Residues in contact with HIS 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 TYR* 2.8 65.9 + + + +
193A MET* 3.2 6.5 + - - +
195A ASP* 1.3 102.6 + - + +
197A PRO* 1.3 68.0 - - - +
198A THR* 3.2 5.4 - - - +
199A ALA* 2.9 21.0 + - + +
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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