Contacts of the helix formed by residues 194 - 204 (chain A) in PDB entry 1QZZ
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 GLY 194 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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191A GLY 3.1 8.3 + - - -
192A GLY 3.2 2.0 + - - -
193A ASN* 1.3 78.1 - - - +
195A GLY* 1.3 55.7 + - - +
196A MET 3.4 2.7 - - - -
197A LEU 3.2 1.2 + - - -
198A ALA* 2.8 36.6 + - - +
211A LEU* 3.6 4.7 - - - -
224A ARG* 3.6 3.8 - - - -
225A PHE* 3.5 22.7 - - - -
421A ACT 3.5 12.6 - - - -
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Residues in contact with GLY 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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171A TYR* 3.5 26.2 - - - +
193A ASN* 3.5 7.4 - - - +
194A GLY* 1.3 75.5 - - - +
196A MET* 1.3 61.9 + - - +
198A ALA* 3.5 2.1 + - - +
199A ALA* 3.1 22.7 + - - +
224A ARG* 3.5 23.6 - - - +
421A ACT 3.5 4.0 - - - +
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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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171A TYR* 3.6 34.5 - - + +
174A PRO* 3.8 11.0 - - + +
175A ALA* 3.6 34.3 - - - +
180A TRP* 4.0 10.8 - - + -
195A GLY* 1.3 71.7 - - - -
197A LEU* 1.3 61.2 + - - +
199A ALA* 3.2 3.6 + - - +
200A ILE* 3.0 41.8 + - + +
253A LEU* 3.8 23.3 - - + -
255A SER* 4.0 2.2 - - - +
286A LEU* 3.8 17.7 - - + -
350A ILE* 4.9 4.7 - - + -
421A ACT 2.9 32.3 - - + +
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Residues in contact with LEU 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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186A VAL* 4.1 32.1 - - + -
188A ASP* 3.4 35.8 + - + +
194A GLY 3.2 4.9 + - - +
196A MET* 1.3 76.2 - - - +
198A ALA* 1.3 52.5 + - - +
200A ILE* 3.2 14.0 + - + +
201A ALA* 2.7 37.2 + - + +
207A LEU* 5.0 5.6 - - + -
209A GLY* 4.4 9.0 - - - -
210A THR 4.3 9.6 - - - +
211A LEU* 4.0 8.3 - - + -
225A PHE* 3.9 11.0 - - + -
234A VAL* 3.5 31.6 - - + -
253A LEU* 5.1 0.4 - - + +
421A ACT 3.1 7.5 + - - +
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Residues in contact with ALA 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 GLY 2.8 17.3 + - - +
195A GLY* 3.7 4.3 - - - +
197A LEU* 1.3 75.1 - - - +
199A ALA* 1.3 66.2 + - - +
201A ALA* 3.7 0.5 - - - +
202A LEU* 2.9 36.0 + - + +
224A ARG* 4.3 15.9 - - + +
225A PHE* 4.1 9.1 - - + -
228A ALA* 5.3 4.0 - - + -
230A LEU* 3.9 22.0 - - + -
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Residues in contact with ALA 199 (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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171A TYR* 4.1 16.4 - - + +
172A GLU* 4.5 5.2 - - - +
175A ALA* 3.8 12.8 - - + -
195A GLY 3.1 14.8 + - - +
196A MET 3.2 4.7 + - - +
198A ALA* 1.3 78.8 - - - +
200A ILE* 1.3 58.9 + - - +
202A LEU* 4.0 5.9 - - - +
203A ARG* 2.7 56.3 + - - +
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Residues in contact with ILE 200 (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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175A ALA* 4.6 1.8 - - + -
180A TRP* 3.5 66.4 - - + +
186A VAL* 4.6 11.0 - - + -
196A MET* 3.0 41.5 + - + +
197A LEU* 3.4 12.1 - - + +
199A ALA* 1.3 74.1 - - - +
201A ALA* 1.3 68.9 + - - +
202A LEU 3.1 1.1 - - - -
203A ARG* 3.0 9.7 + - - +
204A ALA* 2.9 21.0 + - + +
207A LEU* 4.5 15.7 - - + -
253A LEU* 4.0 13.0 - - + -
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Residues in contact with ALA 201 (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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197A LEU* 2.7 20.5 + - + +
198A ALA 3.8 0.2 - - - +
200A ILE* 1.3 75.4 - - - +
202A LEU* 1.3 62.4 + - - +
204A ALA 3.2 13.1 + - - +
207A LEU* 4.9 8.5 - - + -
230A LEU* 3.6 30.1 - - + -
233A ARG* 2.8 32.1 + - - +
234A VAL* 4.0 17.0 - - + -
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Residues in contact with LEU 202 (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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172A GLU* 6.0 1.6 - - - +
198A ALA* 2.9 26.4 + - + +
199A ALA* 4.0 7.2 - - - +
201A ALA* 1.3 79.7 - - - +
203A ARG* 1.3 63.5 + - - +
204A ALA 3.5 0.5 + - - -
205A PRO* 4.6 8.7 - - - +
228A ALA* 4.3 24.0 - - + +
230A LEU* 4.3 20.0 - - + -
233A ARG* 4.6 2.1 + - - +
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Residues in contact with ARG 203 (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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172A GLU* 2.5 34.1 + - - -
175A ALA* 3.6 27.7 - - - +
176A ASP* 3.1 31.7 + - - +
180A TRP* 4.8 10.7 - - + +
181A SER* 6.1 0.3 - - - -
199A ALA* 2.7 46.4 + - - +
200A ILE* 3.0 9.1 + - - +
202A LEU* 1.3 84.8 - - - +
204A ALA* 1.3 58.5 + - - +
205A PRO* 3.6 8.1 - - - +
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Residues in contact with ALA 204 (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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180A TRP* 3.9 31.9 - - + +
181A SER* 5.3 2.7 - - - +
200A ILE 2.9 11.6 + - - +
201A ALA 3.2 4.7 - - - +
202A LEU 3.3 1.0 - - - -
203A ARG* 1.3 79.4 - - - +
205A PRO* 1.3 69.1 - - - +
206A HIS 3.1 2.2 - - - -
207A LEU* 3.0 26.9 + - + +
233A ARG* 2.9 14.4 + - - -
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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