Contacts of the helix formed by residues 187 - 199 (chain O) in PDB entry 3H1J
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 THR 187 (chain O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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137O VAL* 5.1 1.3 - - - -
185O LYS 3.8 8.3 - - - +
186O ILE* 1.3 76.2 - - - +
188O SER* 1.3 64.2 + - - +
189O GLU* 3.1 22.1 + - - +
190O GLN* 3.0 40.1 + - + +
191O LEU* 3.2 22.0 + - - +
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Residues in contact with SER 188 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132O PHE* 2.8 29.6 + - - -
134O PRO* 3.7 19.9 - - - +
137O VAL* 3.6 18.3 - - - +
187O THR* 1.3 70.7 - - - +
189O GLU* 1.3 78.4 + - - +
191O LEU* 3.0 10.6 + - - +
192O HIS* 2.8 33.6 + - - -
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Residues in contact with GLU 189 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134O PRO* 6.1 0.3 - - - +
187O THR* 3.3 19.0 + - - +
188O SER* 1.3 85.7 + - - +
190O GLN* 1.3 57.2 + - + +
192O HIS* 3.0 8.3 + - - +
193O HIS* 2.8 58.9 + - + +
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Residues in contact with GLN 190 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61O ALA* 3.2 12.5 + - - +
62O ASN* 3.1 41.0 + - + +
65O THR* 3.8 12.5 + - - +
182O ARG* 2.9 20.6 + - - +
185O LYS 3.5 4.0 - - - +
186O ILE* 3.4 4.2 - - + -
187O THR* 3.0 40.3 + - + +
189O GLU* 1.3 77.8 - - + +
191O LEU* 1.3 62.1 + - - +
193O HIS* 3.9 6.4 - - + +
194O PHE* 2.9 26.2 + - - +
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Residues in contact with LEU 191 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65O THR* 3.5 32.3 - - - +
68O LEU* 4.2 16.8 - - + -
69O LEU* 4.2 14.7 - - + +
72O ALA* 4.8 7.9 - - + -
75O LEU* 5.7 0.4 - - + -
132O PHE* 3.4 42.6 - - + -
137O VAL* 4.2 18.8 - - + -
186O ILE* 4.1 13.0 - - + -
187O THR 3.2 12.1 + - - +
188O SER* 3.0 6.3 + - - +
190O GLN* 1.3 79.1 - - - +
192O HIS* 1.3 64.1 + - - +
194O PHE* 3.4 3.8 - - - +
195O VAL* 3.1 24.9 + - - +
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Residues in contact with HIS 192 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78O LYS* 5.4 5.0 + - - -
130O PRO* 4.0 11.0 + - + -
131O GLU* 3.0 33.5 + - - -
132O PHE* 3.6 24.3 - + + -
188O SER* 2.8 27.2 + - - -
189O GLU* 3.5 9.2 + - - +
191O LEU* 1.3 72.7 - - - +
193O HIS* 1.3 72.2 + - + +
195O VAL* 2.9 6.5 + - + +
196O GLN* 2.8 46.1 + - + +
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Residues in contact with HIS 193 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189O GLU* 2.8 50.2 + - + +
190O GLN* 4.1 5.2 - - + +
192O HIS* 1.3 77.0 - - + +
194O PHE* 1.3 56.8 + - - +
196O GLN* 3.0 29.1 + - - -
197O ASN* 2.8 49.0 + - - +
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Residues in contact with PHE 194 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53O ALA* 4.2 17.0 - - + -
54O GLY 3.7 30.7 - - - -
57O TYR* 4.3 10.5 - - + -
58O GLU* 4.4 15.7 - - + -
62O ASN* 4.1 10.8 - - - +
65O THR* 4.1 22.7 - - + +
66O ALA* 4.0 13.7 - - + -
69O LEU* 3.5 29.6 - - + -
105O MET* 4.7 2.0 - - - -
190O GLN 2.9 19.8 + - - +
191O LEU* 3.4 5.6 - - - +
192O HIS 3.0 0.2 - - - -
193O HIS* 1.3 77.3 - - - +
195O VAL* 1.3 60.8 + - - +
197O ASN* 4.9 0.7 - - - +
198O ASN* 2.9 52.2 + - - +
199O PHE* 4.3 2.0 - + - -
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Residues in contact with VAL 195 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69O LEU* 4.0 17.7 - - + -
127O THR 4.5 2.7 - - - +
130O PRO* 4.6 13.2 - - + -
132O PHE* 3.8 24.5 - - + -
191O LEU 3.1 14.4 + - - +
192O HIS* 2.9 9.3 + - + +
194O PHE* 1.3 75.3 - - - +
196O GLN* 1.3 61.4 + - + +
199O PHE* 2.6 66.6 + - + +
226O ILE* 4.2 14.9 - - + +
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Residues in contact with GLN 196 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192O HIS* 2.8 45.5 + - + +
193O HIS* 3.0 31.5 + - - +
195O VAL* 1.3 75.8 - - + +
197O ASN* 1.3 66.8 + - - +
198O ASN 3.5 0.5 + - - -
200O THR* 3.8 14.0 - - - +
226O ILE* 5.0 7.1 - - - +
227O ARG* 3.9 17.2 - - + +
231O GLY* 5.4 0.5 - - - -
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Residues in contact with ASN 197 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193O HIS* 2.8 41.7 + - - +
194O PHE* 4.2 1.7 - - - +
196O GLN* 1.3 79.2 - - - +
198O ASN* 1.3 67.6 + - - +
200O THR* 4.1 4.0 - - - -
230O ALA 4.1 0.5 - - - +
231O GLY* 3.4 8.0 - - - -
232O THR* 2.9 51.2 + - - +
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Residues in contact with ASN 198 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51O ILE* 4.0 4.5 - - - +
53O ALA* 4.4 7.9 - - + -
57O TYR* 3.5 13.8 - - - +
194O PHE* 2.9 53.6 + - + +
195O VAL 3.2 0.2 + - - -
196O GLN 3.3 0.4 - - - -
197O ASN* 1.3 92.3 - - - +
199O PHE* 1.3 67.9 + - + +
200O THR* 2.8 11.5 + - - -
203O ARG* 2.7 54.4 + - - +
232O THR* 3.5 13.4 - - - +
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Residues in contact with PHE 199 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51O ILE* 3.3 33.9 - - + -
53O ALA* 3.4 23.8 - - + -
69O LEU* 3.5 32.3 - - + -
105O MET* 3.9 12.1 - - - -
107O TYR* 4.0 19.7 - + - -
126O VAL 5.9 0.4 - - - -
127O THR* 3.7 20.9 - - - -
194O PHE* 4.3 5.4 - + - -
195O VAL* 2.6 44.9 + - + +
198O ASN* 1.3 75.2 - - + +
200O THR* 1.3 52.9 + - - +
204O MET* 3.4 20.5 - - - +
226O ILE* 2.8 31.8 - - + +
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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