Contacts of the helix formed by residues 203 - 213 (chain M) in PDB entry 3HOU
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 203 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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201M VAL* 3.3 9.2 + - - -
202M LEU* 1.3 73.7 - - - +
204M THR* 1.3 60.1 + - - +
205M GLU* 3.2 19.2 + - - +
206M GLU* 2.7 34.2 + - - +
207M ILE* 2.9 30.4 + - - +
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Residues in contact with THR 204 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89M PRO* 2.7 55.3 + - + +
90M VAL* 3.8 5.2 - - - +
91M PHE* 3.5 28.2 + - + -
202M LEU 3.9 0.6 + - - -
203M SER* 1.3 70.3 + - - +
205M GLU* 1.3 70.7 + - - +
206M GLU 2.8 4.8 + - - -
207M ILE* 2.9 8.0 + - - +
208M LEU* 2.7 23.4 + - - +
235M ILE* 4.0 9.9 - - + -
293M GLU* 5.1 1.8 - - - -
297M GLN* 5.2 1.2 + - - -
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Residues in contact with GLU 205 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88M LYS* 3.1 35.2 + - + +
89M PRO* 3.6 27.7 - - + +
203M SER* 3.5 13.0 + - - +
204M THR* 1.3 85.3 + - - +
206M GLU* 1.3 60.0 + - - +
208M LEU* 3.8 6.3 - - - +
209M ASN* 3.2 22.7 + - - +
293M GLU* 3.3 19.8 - - - +
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Residues in contact with GLU 206 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108M MET* 5.6 1.0 - - - +
185M TRP* 5.2 0.5 - - - -
200M ARG* 2.8 32.0 + - - -
201M VAL 4.1 0.6 - - - +
202M LEU* 3.0 29.2 - - - +
203M SER* 2.7 46.9 + - - +
204M THR 2.8 0.4 + - - -
205M GLU* 1.3 75.9 - - - +
207M ILE* 1.3 66.1 + - + +
209M ASN* 3.2 6.1 + - - +
210M ILE* 3.1 34.1 + - + +
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Residues in contact with ILE 207 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91M PHE* 4.0 16.2 - - + -
99M ILE* 4.0 10.3 - - + -
103M CYS* 3.6 16.8 - - - -
108M MET* 3.9 24.2 - - + -
181M LEU* 4.5 5.4 - - + -
202M LEU* 3.5 36.3 - - + +
203M SER 2.9 17.2 + - - +
204M THR 2.9 5.3 + - - +
206M GLU* 1.3 69.7 - - - +
208M LEU* 1.3 66.9 + - - +
210M ILE* 3.4 1.9 + - - +
211M PHE* 3.1 49.4 + - + -
235M ILE* 4.3 4.5 - - + -
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Residues in contact with LEU 208 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89M PRO* 4.0 25.8 - - + -
204M THR 2.7 14.9 + - - +
205M GLU* 3.8 6.5 - - - +
207M ILE* 1.3 77.6 - - - +
209M ASN* 1.3 63.8 + - - +
211M PHE* 3.1 5.0 + - - +
212M LYS* 2.9 57.1 + - + +
232M GLU* 4.1 13.5 - - + +
235M ILE* 3.2 32.2 - - + +
237M THR* 4.4 10.3 - - - +
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Residues in contact with ASN 209 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205M GLU 3.2 13.6 + - - +
206M GLU* 3.2 6.3 + - - +
208M LEU* 1.3 82.7 - - - +
210M ILE* 1.3 64.8 + - + +
212M LYS* 3.2 15.4 + - - +
213M HIS* 3.0 45.9 + - - +
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Residues in contact with ILE 210 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106M VAL* 4.3 7.4 - - + -
107M CYS 3.9 17.0 - - - +
108M MET* 3.0 62.4 - - + -
109M HIS* 3.1 14.6 - - - +
110M CYS 6.2 0.2 - - - -
111M GLY* 4.1 8.6 - - - -
206M GLU* 3.1 21.5 + - + +
207M ILE 3.9 6.1 - - - +
208M LEU 3.3 0.4 - - - -
209M ASN* 1.3 76.1 - - + +
211M PHE* 1.3 68.2 + - + +
213M HIS* 3.1 16.1 + - - +
214M ILE* 3.2 12.3 + - + +
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Residues in contact with PHE 211 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99M ILE* 3.3 43.7 - - + -
102M VAL* 3.0 35.7 - - + -
103M CYS* 3.6 12.6 - - - -
106M VAL* 5.5 0.7 - - + -
207M ILE* 3.1 39.5 + - + -
208M LEU 3.1 6.8 + - - +
210M ILE* 1.3 79.2 - - + +
212M LYS* 1.3 59.5 + - - +
214M ILE* 2.9 43.7 + - + +
219M PHE* 4.6 3.3 - - - -
231M PRO* 4.1 16.4 - - + +
232M GLU* 4.0 24.2 - - - +
234M MET* 5.1 2.7 - - + -
235M ILE* 4.1 10.5 - - + -
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Residues in contact with LYS 212 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208M LEU* 2.9 41.4 + - + +
209M ASN* 3.4 19.7 - - - +
211M PHE* 1.3 76.2 - - - +
213M HIS* 1.3 67.8 + - + +
214M ILE 3.6 5.0 + - - +
219M PHE* 5.8 1.6 - - - -
232M GLU* 4.0 30.2 - - + +
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Residues in contact with HIS 213 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109M HIS 5.7 4.9 - - - -
110M CYS 4.3 16.7 - - - +
111M GLY* 3.5 8.6 - - - +
209M ASN* 3.0 32.4 + - - +
210M ILE* 3.1 11.0 + - - +
211M PHE 3.0 0.2 - - - -
212M LYS* 1.3 82.4 + - + +
214M ILE* 1.3 65.5 + - - +
215M SER* 3.2 4.2 + - - -
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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