Contacts of the helix formed by residues 200 - 212 (chain A) in PDB entry 3M3D
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 SER 200 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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117A GLY* 3.4 11.1 - - - -
118A GLY 3.6 6.8 + - - -
119A GLY 4.6 1.8 + - - -
199A GLU* 1.3 86.4 + - - +
201A ALA* 1.3 66.1 + - - -
203A GLY* 2.7 4.0 + - - -
204A ALA* 2.7 28.8 + - - +
225A GLN 2.7 13.7 + - - -
226A SER 3.2 15.7 + - - -
227A GLY* 3.8 2.6 - - - -
233A TRP* 3.8 10.5 - - - -
288A PHE* 6.4 0.2 - - - -
440A HIS* 3.2 30.7 - - - -
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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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116A TYR 4.5 0.7 - - - -
117A GLY* 4.2 2.0 - - - -
118A GLY 4.1 5.4 - - - +
119A GLY* 3.5 27.6 - - - +
120A PHE* 3.6 33.6 - - + +
148A TYR* 4.7 2.5 - - - +
200A SER* 1.3 81.9 + - - +
202A GLY* 1.3 50.2 + - - +
204A ALA* 4.1 1.6 - - - -
205A SER* 2.8 38.2 + - - -
233A TRP* 3.6 14.7 - - + -
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Residues in contact with GLY 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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115A ILE* 3.3 26.2 - - - +
116A TYR 3.5 7.0 - - - -
117A GLY* 3.6 4.0 - - - -
198A GLY* 3.6 7.5 - - - -
199A GLU 2.9 8.8 + - - -
201A ALA* 1.3 75.5 - - - +
203A GLY* 1.3 57.6 + - - +
205A SER* 3.3 8.0 + - - -
206A VAL* 3.0 30.1 + - - +
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Residues in contact with GLY 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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198A GLY 3.3 23.9 - - - -
199A GLU* 3.3 2.8 - - - +
200A SER 2.7 13.2 + - - -
202A GLY* 1.3 70.1 - - - +
204A ALA* 1.3 64.4 + - - -
206A VAL* 3.2 6.1 + - - +
207A GLY 3.1 17.5 + - - -
224A LEU* 3.2 25.2 - - - +
225A GLN 4.4 2.5 - - - -
227A GLY 4.1 4.7 - - - -
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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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120A PHE* 4.5 3.8 - - + -
200A SER 2.7 16.0 + - - +
201A ALA* 3.6 12.8 - - - +
203A GLY* 1.3 71.9 - - - -
205A SER* 1.3 64.0 + - - +
207A GLY* 3.2 3.3 + - - -
208A MET* 2.9 28.3 + - + +
228A SER 3.4 33.7 - - - +
229A PRO* 3.9 3.5 - - + +
233A TRP* 4.2 10.3 - - + -
234A ALA* 4.2 12.3 - - + -
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Residues in contact with SER 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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115A ILE* 4.2 3.6 - - - -
120A PHE* 3.4 13.9 - - - -
148A TYR* 4.7 0.5 + - - -
170A LEU* 4.0 3.1 - - - +
173A GLN* 3.0 39.7 + - - -
201A ALA 2.8 24.5 + - - -
202A GLY* 3.5 9.3 - - - -
203A GLY 3.2 0.2 - - - -
204A ALA* 1.3 74.3 - - - +
206A VAL* 1.3 64.5 + - - +
208A MET* 2.9 22.3 + - - +
209A HIS* 3.0 20.3 + - - -
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Residues in contact with VAL 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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115A ILE* 4.3 7.9 - - + -
196A ILE* 3.8 19.9 - - + +
197A PHE* 3.8 14.1 - - - +
198A GLY 3.8 20.9 - - - +
202A GLY 3.0 17.1 + - - +
203A GLY 3.5 7.9 - - - +
205A SER* 1.3 75.6 - - - +
207A GLY* 1.3 63.3 + - - +
209A HIS* 3.1 17.1 + - - +
210A ILE* 3.1 12.1 + - + +
222A ALA* 3.5 32.1 - - + -
223A ILE 3.8 7.6 - - - +
224A LEU* 3.7 14.8 - - + -
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Residues in contact with GLY 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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203A GLY 3.1 7.5 + - - -
204A ALA 3.6 3.8 - - - -
206A VAL* 1.3 76.8 - - - +
208A MET* 1.3 62.5 + - - +
210A ILE* 3.3 14.1 + - - +
211A LEU* 3.1 27.5 + - - +
224A LEU* 3.7 13.0 - - - +
229A PRO* 3.8 20.0 - - - +
407A PHE* 4.8 2.8 - - - -
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Residues in contact with MET 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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120A PHE* 4.4 4.0 - - + -
170A LEU* 4.1 13.9 - - + -
204A ALA* 2.9 16.0 + - + +
205A SER* 2.9 16.1 + - - +
207A GLY* 1.3 77.6 - - - +
209A HIS* 1.3 56.5 + - - +
211A LEU* 3.2 5.5 + - - +
212A SER* 2.9 31.0 + - - -
229A PRO* 3.7 29.4 - - + +
234A ALA* 3.5 32.8 - - + +
235A SER* 4.6 4.7 - - - -
294A PRO* 3.9 22.7 - - + -
300A PHE* 3.8 8.4 - - + -
301A PHE* 3.4 35.9 - - + -
305A LEU* 5.2 2.2 - - + -
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Residues in contact with HIS 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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115A ILE* 4.3 12.1 - - + -
170A LEU* 3.6 24.5 - - + +
173A GLN* 2.7 34.6 + - + +
174A ARG* 4.1 9.9 - - + -
177A LEU* 4.4 9.8 - - + +
196A ILE* 4.0 3.6 - - + -
205A SER 3.0 25.0 + - - -
206A VAL* 3.1 8.5 + - - +
208A MET* 1.3 73.4 - - - +
210A ILE* 1.3 65.6 + - - +
212A SER 3.6 4.7 - - - +
215A SER* 2.7 36.3 + - - -
216A ARG* 3.6 23.0 + - - -
219A PHE* 3.6 17.5 - - + -
300A PHE* 3.9 13.0 - + - -
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Residues in contact with ILE 210 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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206A VAL* 3.1 17.9 + - + +
207A GLY* 3.4 17.0 - - - +
208A MET 3.2 0.2 - - - -
209A HIS* 1.3 81.0 - - - +
211A LEU* 1.3 61.8 + - + +
216A ARG* 3.4 5.5 + - - -
219A PHE* 3.9 21.5 - - + -
222A ALA* 3.6 24.2 - - + -
224A LEU* 4.5 2.5 - - + -
314A PHE* 4.1 6.3 - - + -
315A LYS* 3.0 42.9 + - + +
317A THR* 5.6 1.3 - - + -
319A ILE* 4.2 17.7 - - + -
407A PHE* 4.5 12.6 - - + -
411A TYR* 3.8 26.2 - - + +
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Residues in contact with LEU 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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207A GLY 3.1 17.9 + - - +
208A MET* 3.2 8.0 + - - +
210A ILE* 1.3 79.0 - - + +
212A SER* 1.3 61.0 + - - +
213A PRO 3.2 0.9 - - - -
216A ARG* 2.8 28.4 + - - -
229A PRO* 3.6 27.4 - - + -
301A PHE* 4.7 5.8 - - + -
305A LEU* 4.0 22.7 - - + +
308A MET* 3.3 46.8 - - + +
309A LEU* 4.5 20.6 - - + -
313A ASN 4.1 5.4 - - - +
314A PHE* 4.1 12.6 - - + -
407A PHE* 5.5 1.6 - - + -
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Residues in contact with SER 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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174A ARG* 3.1 19.6 + - - -
208A MET 2.9 11.8 + - - -
209A HIS 3.6 1.6 + - - +
210A ILE 3.7 0.2 - - - -
211A LEU* 1.3 70.3 - - - +
213A PRO* 1.3 72.7 - - - +
214A GLY 3.9 1.6 + - - -
215A SER* 2.9 23.7 + - - -
216A ARG* 3.1 12.7 + - - +
299A GLU 4.7 0.2 + - - -
300A PHE* 2.5 51.0 + - - -
301A PHE* 5.1 0.8 - - - -
308A MET* 5.2 0.4 - - - -
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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