Contacts of the strand formed by residues 229 - 237 (chain E) in PDB entry 1HGH
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 ARG 229 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206A THR 4.2 8.5 + - - -
207A ARG 4.4 7.5 + - - -
209A SER 5.9 0.8 + - - -
210A GLN* 4.3 21.9 - - + +
98E TYR* 4.2 1.3 - - - -
99E PRO* 3.4 34.9 - - - +
100E TYR* 4.7 5.6 - - - +
101E ASP* 4.7 3.1 - - - +
183E HIS* 3.8 2.1 - - - -
184E HIS* 2.9 33.9 + - + +
220E ARG* 3.6 36.4 - - + +
221E PRO* 2.6 30.5 + - - +
223E VAL* 3.5 14.8 - - - +
226E LEU 3.4 20.4 + - - -
227E SER 3.8 4.2 - - - -
228E SER* 1.3 99.5 + - - +
230E ILE* 1.3 69.2 + - - +
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Residues in contact with ILE 230 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98E TYR* 3.7 22.0 - - + -
99E PRO 3.1 8.9 + - - +
100E TYR* 3.0 21.4 - - + +
101E ASP* 2.9 24.4 + - - +
147E PHE* 3.8 15.0 - - + -
148E PHE* 3.7 29.4 - - + -
151E LEU* 4.5 0.2 - - + -
182E ILE 3.2 13.0 - - - +
183E HIS* 3.9 19.1 - - + -
184E HIS* 4.5 0.2 - - - -
229E ARG* 1.3 77.9 - - - +
231E SER* 1.3 60.1 + - - +
232E ILE* 3.9 18.2 - - + -
252E ILE* 4.4 18.6 - - + -
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Residues in contact with SER 231 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210A GLN* 3.7 1.9 + - - -
101E ASP* 2.9 28.6 + - - -
103E PRO* 4.2 5.5 - - - +
181E GLY* 3.1 5.4 - - - -
182E ILE* 3.1 28.9 + - - -
184E HIS* 2.8 28.8 + - - -
230E ILE* 1.3 72.4 - - - +
232E ILE* 1.3 60.4 + - - +
233E TYR* 3.8 26.4 + - - -
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Residues in contact with ILE 232 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71E LEU* 3.8 28.9 - - + -
100E TYR* 3.9 16.8 - - + -
101E ASP 2.9 6.5 + - - -
102E VAL* 3.6 26.8 - - + +
103E PRO* 3.5 20.3 - - - +
108E LEU* 4.3 9.0 - - + -
151E LEU* 3.8 29.4 - - + -
179E ILE* 3.5 25.8 - - + -
180E TRP 3.6 5.4 - - - +
181E GLY* 4.9 2.0 - - - -
230E ILE* 3.9 20.0 - - + -
231E SER* 1.3 74.8 - - - +
233E TYR* 1.3 68.3 + - - +
234E TRP* 5.5 0.2 - - - -
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Residues in contact with TYR 233 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103E PRO* 3.6 35.1 - - + +
179E ILE* 3.6 8.1 - - - +
180E TRP* 2.9 69.9 + + + +
181E GLY* 4.3 1.1 - - - -
182E ILE* 4.0 9.6 - - + -
184E HIS* 5.5 0.9 + - - -
211E GLN* 4.4 11.0 - - - +
213E ILE* 3.5 38.9 - - + +
231E SER* 3.8 29.3 + - - -
232E ILE* 1.3 76.1 - - - +
234E TRP* 1.3 69.4 + - - +
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Residues in contact with TRP 234 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73D VAL 3.8 13.7 - - - -
74D GLU* 4.6 11.9 - - - -
102E VAL* 5.5 2.7 - - + -
104E ASP* 5.0 10.2 + - - +
107E SER* 4.8 7.3 - - - -
108E LEU* 3.7 34.8 - - + +
111E LEU* 3.3 34.5 - - + -
177E LEU* 4.1 5.4 - - + -
178E TYR 3.2 7.6 - - - +
179E ILE* 3.7 20.2 - - + -
180E TRP* 4.1 0.9 - - - +
211E GLN* 3.8 14.7 + - - +
232E ILE 5.5 1.1 - - - -
233E TYR* 1.3 82.1 - - - +
235E THR* 1.3 66.1 + - - +
236E ILE* 3.7 32.5 - - + -
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Residues in contact with THR 235 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176E LYS 3.7 0.9 - - - +
178E TYR* 2.9 34.0 + - - +
180E TRP* 2.9 25.2 + - - -
204E VAL* 3.6 9.2 - - + +
205E SER 5.4 1.3 - - - -
206E THR* 4.1 19.1 - - + -
209E SER* 4.9 7.6 - - - +
211E GLN* 3.3 15.2 + - - +
234E TRP* 1.3 75.0 + - - +
236E ILE* 1.3 66.6 + - - +
237E VAL* 3.9 1.9 + - + -
243E LEU* 3.8 26.2 - - + -
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Residues in contact with ILE 236 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72D GLU* 6.1 0.9 - - - +
73D VAL* 4.0 27.6 - - + +
111E LEU* 4.4 2.5 - - + -
175E ASP* 3.9 29.4 - - + +
176E LYS 3.2 9.0 - - - +
177E LEU* 3.9 13.9 - - + -
206E THR* 4.4 4.9 + - - +
234E TRP* 3.7 28.2 - - + -
235E THR* 1.3 80.1 - - - +
237E VAL* 1.3 63.7 + - - +
238E LYS* 4.1 6.5 + - + +
260E MET* 3.6 25.8 - - + -
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Residues in contact with VAL 237 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168E MET 5.1 0.9 - - - +
170E ASN* 2.9 39.9 + - + +
175E ASP* 3.5 0.9 - - - -
176E LYS* 2.7 27.3 + - + +
178E TYR* 3.6 35.9 - - + -
206E THR* 3.8 19.5 - - + -
235E THR* 4.2 1.8 - - + -
236E ILE* 1.3 76.9 - - - +
238E LYS* 1.3 64.3 + - - +
241E ASP* 4.0 13.5 - - + -
242E VAL* 4.1 14.4 - - - +
243E LEU* 4.0 13.9 - - + +
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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