Contacts of the helix formed by residues 184 - 198 (chain A) in PDB entry 4Z2C
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 184 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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97A ARG* 3.9 1.8 - - - +
98A TYR* 3.5 14.6 + - - -
183A HIS* 1.3 72.8 - - - +
185A LEU* 1.3 61.1 + - - +
186A GLY* 3.0 10.1 + - - -
187A GLU* 3.0 53.8 + - - +
188A THR* 2.6 33.7 + - - -
214A ASP* 3.5 29.1 + - + +
477A SER* 3.9 1.9 + - - -
478A ASP 3.2 28.4 + - - +
479A LYS 4.3 4.2 - - - -
480A ARG* 4.4 3.8 - - - +
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Residues in contact with LEU 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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98A TYR* 3.0 35.0 + - + +
128A ILE* 4.2 11.2 - - + -
161A PHE* 4.1 19.5 - - + -
162A PRO* 4.8 0.2 - - + -
166A VAL* 4.0 19.7 - - + -
183A HIS 3.7 0.6 + - - -
184A ASN* 1.3 73.3 - - - +
186A GLY* 1.3 65.1 + - - +
188A THR* 3.1 1.6 + - - -
189A ILE* 2.9 49.6 + - + +
472A VAL* 4.5 10.8 - - + +
473A LYS* 4.8 1.6 - - - -
476A PHE* 3.7 40.2 - - + +
477A SER* 3.9 8.1 - - - +
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Residues in contact with GLY 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 ASN* 3.0 6.6 + - - -
185A LEU* 1.3 79.2 - - - +
187A GLU* 1.3 55.5 + - - +
189A ILE* 3.5 2.4 + - - +
190A ASP* 2.9 39.2 + - - +
473A LYS* 3.8 24.0 - - - +
477A SER* 3.1 17.8 + - - -
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Residues in contact with GLU 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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184A ASN* 3.0 34.2 + - - +
186A GLY* 1.3 73.9 - - - +
188A THR* 1.3 59.9 + - - +
190A ASP* 3.1 9.3 + - - +
191A ALA* 2.9 28.4 + - - +
209A VAL 3.4 20.1 - - - +
210A LEU* 3.8 15.3 - - + +
211A PRO* 3.3 18.9 - - - +
212A GLY 4.1 1.0 - - - +
480A ARG* 2.6 46.1 + - - +
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Residues in contact with THR 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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162A PRO* 3.6 26.9 - - + -
165A LEU* 3.9 30.1 - - + -
166A VAL* 3.5 10.5 - - + +
183A HIS* 3.4 19.2 - - - +
184A ASN 2.6 23.3 + - - -
185A LEU 3.6 3.4 - - - -
187A GLU* 1.3 75.7 - - - +
189A ILE* 1.3 58.5 + - - +
191A ALA* 3.3 3.2 + - - +
192A VAL* 2.9 27.3 + - - +
210A LEU* 4.2 13.7 - - + +
348A LEU* 4.5 4.9 - - + +
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Residues in contact with ILE 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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162A PRO* 4.2 9.9 - - + -
185A LEU* 2.9 38.3 + - + +
186A GLY* 3.7 4.9 - - - +
188A THR* 1.3 74.3 - - - +
190A ASP* 1.3 60.3 + - - +
192A VAL* 3.2 6.7 + - - +
193A LYS* 2.9 41.4 + - + +
469A LEU* 3.5 61.2 - - + +
470A ASP* 4.7 0.2 - - - +
472A VAL* 4.2 4.7 - - + -
473A LYS* 3.6 27.8 - - + +
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Residues in contact with ASP 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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186A GLY 2.9 28.4 + - - +
187A GLU* 3.1 10.6 + - - +
189A ILE* 1.3 76.5 - - - +
191A ALA* 1.3 57.2 + - - +
193A LYS* 3.8 12.9 + - - +
194A LEU* 2.9 30.5 + - - +
209A VAL* 4.2 24.3 - - + +
473A LYS* 2.8 30.3 + - - +
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Residues in contact with ALA 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 GLU 2.9 12.7 + - - +
188A THR 3.5 8.1 - - - +
190A ASP* 1.3 74.5 - - - +
192A VAL* 1.3 59.3 + - - +
194A LEU* 3.2 7.4 + - - +
195A VAL* 2.9 31.2 + - - +
206A LEU* 3.7 20.2 - - + +
209A VAL* 4.1 7.5 - - + +
210A LEU* 4.1 24.5 - - + -
348A LEU* 4.2 13.4 - - + +
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Residues in contact with VAL 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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162A PRO* 5.5 2.7 - - + -
188A THR 2.9 14.7 + - - +
189A ILE* 3.5 11.9 - - - +
191A ALA* 1.3 76.1 - - - +
193A LYS* 1.3 57.3 + - - +
195A VAL* 3.4 2.1 + - - -
196A MET* 2.9 34.8 + - + +
348A LEU* 4.4 15.2 - - + +
351A TYR* 4.9 11.2 - - + -
352A ILE* 3.8 18.0 - - + +
469A LEU* 4.3 15.7 - - + -
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Residues in contact with LYS 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 ILE* 2.9 32.0 + - + +
190A ASP* 3.9 13.6 + - - +
192A VAL* 1.3 73.1 - - - +
194A LEU* 1.3 60.5 + - - +
196A MET* 3.2 10.5 + - - +
197A ASP* 2.9 38.1 + - - +
466A LYS* 4.3 27.8 - - + +
469A LEU* 4.4 10.1 - - + -
470A ASP* 2.6 42.0 + - - +
473A LYS* 5.2 2.8 - - - +
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Residues in contact with LEU 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 ASP 2.9 19.9 + - - +
191A ALA 3.3 5.6 - - - +
193A LYS* 1.3 75.9 - - - +
195A VAL* 1.3 57.7 + - - +
197A ASP* 3.1 5.0 + - - +
198A ASN* 2.9 35.2 + - + +
201A VAL* 4.8 7.6 - - + -
205A ASP* 3.5 34.3 - - + +
206A LEU* 3.8 20.6 - - + +
209A VAL* 3.8 17.3 - - + -
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Residues in contact with VAL 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 ALA 2.9 16.2 + - - +
192A VAL 3.8 4.0 - - - +
194A LEU* 1.3 76.6 - - - +
196A MET* 1.3 62.6 + - - +
197A ASP 3.5 0.2 + - - -
198A ASN 3.6 16.3 - - - +
199A PRO* 3.7 13.6 - - - +
201A VAL* 5.3 2.7 - - + -
206A LEU* 4.8 6.0 - - + +
345A ARG* 4.4 26.7 + - - +
348A LEU* 4.7 11.0 - - + -
349A ASP* 4.9 2.0 - - - +
352A ILE* 4.2 14.8 - - + -
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Residues in contact with MET 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 VAL* 2.9 19.7 + - - +
193A LYS* 3.4 12.8 - - - +
194A LEU 3.2 0.2 - - - -
195A VAL* 1.3 79.0 - - - +
197A ASP* 1.3 66.1 + - - +
199A PRO* 5.1 1.9 - - - +
352A ILE* 3.6 35.9 - - + -
356A LYS* 5.3 3.1 - - - -
462A SER* 3.2 51.7 + - - +
465A ILE* 4.1 21.5 - - + -
466A LYS* 3.7 17.3 - - + -
469A LEU* 5.0 5.6 - - - -
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Residues in contact with ASP 197 (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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193A LYS* 2.9 23.7 + - - +
194A LEU* 3.8 3.8 - - - +
196A MET* 1.3 81.8 - - - +
198A ASN* 1.3 60.3 + - + +
199A PRO* 3.1 12.1 - - - +
462A SER* 5.6 0.5 + - - -
466A LYS* 3.7 25.5 - - - +
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Residues in contact with ASN 198 (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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194A LEU* 2.9 22.5 + - + +
195A VAL* 3.6 6.0 - - - +
197A ASP* 1.3 74.5 - - + +
199A PRO* 1.3 65.0 - - + +
200A GLU* 3.3 3.6 - - + +
201A VAL* 3.4 25.8 - - + +
345A ARG* 4.9 0.2 + - - -
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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