Contacts of the helix formed by residues 202 - 215 (chain A) in PDB entry 1MAQ
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 GLN 202 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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200A PRO 4.0 0.6 + - - -
201A ARG* 1.3 71.5 - - - +
203A GLU* 1.3 71.0 + - + +
205A TRP* 3.2 5.7 + - + +
206A LYS* 3.0 31.8 + - - +
235A ARG* 3.4 35.0 + - - +
238A TRP* 3.6 57.3 - - + +
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Residues in contact with GLU 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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201A ARG* 3.7 34.9 + - - +
202A GLN* 1.3 90.1 + - + +
204A GLN* 1.3 64.8 + - + +
206A LYS* 3.3 25.4 + - + +
207A GLU* 3.4 15.1 + - - +
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Residues in contact with GLN 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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168A LEU* 3.3 21.5 - - - +
170A PHE* 3.3 61.8 - - + +
199A ASP 4.4 0.7 - - - +
200A PRO* 3.8 7.0 - - + -
201A ARG* 2.5 80.6 + - + +
203A GLU* 1.3 75.4 - - + +
205A TRP* 1.3 59.6 + - - +
207A GLU* 3.3 2.8 + - - +
208A LEU* 3.3 14.5 + - - +
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Residues in contact with TRP 205 (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 LEU* 3.6 31.6 - - + -
189A HIS 3.5 26.5 - - - -
190A ALA 3.7 14.3 + - - -
199A ASP* 5.0 4.7 - - + +
200A PRO* 3.5 47.6 + - + +
201A ARG 2.8 11.1 + - - -
202A GLN* 3.6 9.4 - - + +
204A GLN* 1.3 75.7 - - - +
206A LYS* 1.3 63.0 + - - +
208A LEU* 3.3 14.9 + - + +
209A ALA* 3.0 23.3 + - - +
221A PHE* 4.1 12.6 - + - -
238A TRP* 3.7 17.3 - + + -
239A ALA* 3.3 21.8 - - + +
242A HIS* 4.9 2.0 - - - +
243A PHE* 3.5 35.6 - + + -
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Residues in contact with LYS 206 (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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202A GLN* 3.0 20.7 + - - +
203A GLU* 3.5 21.5 - - + +
204A GLN 3.2 0.2 - - - -
205A TRP* 1.3 77.1 - - - +
207A GLU* 1.3 58.3 + - - +
209A ALA* 3.3 14.0 - - - +
210A SER* 3.1 16.1 + - - -
238A TRP* 3.5 26.8 - - + -
242A HIS* 3.6 32.1 + - + +
246A GLN* 6.0 0.2 + - - -
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Residues in contact with GLU 207 (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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170A PHE* 4.1 11.4 - - + -
174A MET* 3.2 27.3 - - + +
203A GLU 3.4 8.8 + - - +
204A GLN 3.4 10.8 - - - +
206A LYS* 1.3 77.6 - - - +
208A LEU* 1.3 63.2 + - - +
209A ALA 3.2 0.2 - - - -
210A SER* 3.4 27.0 + - - -
211A VAL* 3.4 12.6 + - - +
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Residues in contact with LEU 208 (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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158A TYR* 5.8 1.3 - - + -
170A PHE* 3.7 28.7 - - + -
173A ALA* 5.5 1.8 - - + -
174A MET* 4.4 9.4 - - - -
177A ILE* 3.4 35.2 - - + -
188A LEU* 4.6 16.4 - - + -
200A PRO* 4.2 16.2 - - + -
204A GLN 3.3 10.3 + - - +
205A TRP* 3.6 24.7 - - + +
207A GLU* 1.3 75.9 - - - +
209A ALA* 1.3 65.8 - - - +
211A VAL* 3.4 4.3 + - + +
212A VAL* 3.0 32.2 + - + +
243A PHE* 4.3 10.8 - - + -
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Residues in contact with ALA 209 (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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205A TRP 3.0 13.2 + - - +
206A LYS 3.3 13.9 - - - +
207A GLU 3.2 0.2 - - - -
208A LEU* 1.3 78.4 - - - +
210A SER* 1.3 63.2 + - - +
212A VAL* 3.1 0.5 + - - +
213A LYS* 2.9 24.4 + - - +
242A HIS* 4.0 20.9 - - + +
243A PHE* 3.9 21.5 - - + -
246A GLN* 4.5 8.3 - - + +
248A ILE* 3.6 14.4 - - + +
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Residues in contact with SER 210 (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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206A LYS 3.1 13.9 + - - -
207A GLU* 3.4 18.8 + - - -
209A ALA* 1.3 77.2 - - - +
211A VAL* 1.3 57.2 + - - -
213A LYS* 3.2 8.2 + - - +
214A LYS* 2.6 38.5 + - - +
246A GLN* 6.1 1.5 - - - +
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Residues in contact with VAL 211 (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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174A MET* 3.8 23.6 - - + +
177A ILE* 4.0 16.2 - - + -
178A SER* 3.9 35.0 - - - +
207A GLU* 3.4 14.9 + - - +
208A LEU* 4.0 7.0 - - - +
209A ALA 3.3 0.4 - - - -
210A SER* 1.3 79.5 - - - +
212A VAL* 1.3 61.1 + - - +
214A LYS* 4.0 19.5 - - - +
215A ARG* 2.9 35.7 + - + +
217A LEU* 4.6 0.2 - - - +
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Residues in contact with VAL 212 (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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177A ILE* 4.5 10.3 - - + -
186A ILE* 4.4 20.0 - - + -
188A LEU* 5.0 3.6 - - + -
208A LEU* 3.0 24.9 + - + +
209A ALA 3.6 3.6 - - - +
211A VAL* 1.3 77.4 - - - +
213A LYS* 1.3 56.5 + - - +
216A ASN* 3.2 5.0 + - - -
217A LEU* 3.0 56.0 + - + +
219A ALA* 4.3 12.1 - - + -
243A PHE* 4.3 13.2 - - + -
248A ILE* 4.2 21.3 - - + +
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Residues in contact with LYS 213 (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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209A ALA 2.9 16.5 + - - +
210A SER* 3.4 7.6 - - - +
212A VAL* 1.3 76.4 - - - +
214A LYS* 1.3 65.2 + - - +
216A ASN* 3.1 16.0 + - - +
246A GLN* 3.3 28.3 + - + +
247A GLY* 3.8 16.1 + - - +
248A ILE* 4.0 20.2 - - + -
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Residues in contact with LYS 214 (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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178A SER* 5.3 7.3 - - - -
182A GLU* 5.2 4.0 - - - +
210A SER 2.6 22.4 + - - +
211A VAL* 3.9 25.8 - - - +
213A LYS* 1.3 75.4 - - - +
215A ARG* 1.3 72.2 + - + +
216A ASN* 3.5 1.9 + - - +
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Residues in contact with ARG 215 (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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177A ILE 4.1 4.9 - - - +
178A SER* 3.3 29.1 + - - +
179A LYS* 3.7 6.0 + - - +
180A ILE 2.4 35.1 + - - -
181A PRO* 3.6 9.9 - - - +
182A GLU* 3.0 46.2 + - + +
211A VAL* 2.9 35.8 + - + +
214A LYS* 1.3 86.8 - - + +
216A ASN* 1.3 74.7 + - - +
217A LEU* 3.8 17.8 - - + +
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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