Contacts of the strand formed by residues 229 - 237 (chain A) in PDB entry 5HMG
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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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98A TYR* 4.5 1.1 - - - -
99A PRO* 3.2 29.8 - - - +
100A TYR 4.7 4.7 - - - +
101A ASP* 4.1 14.6 - - + +
183A HIS* 4.0 1.7 - - - -
184A HIS* 2.9 33.2 + - + +
220A ARG* 3.6 29.5 - - - +
221A PRO 2.7 33.5 + - - -
223A VAL* 3.2 19.8 - - - +
226A LEU 3.4 13.5 + - - -
227A SER 3.8 3.2 - - - -
228A SER* 1.3 101.8 + - - +
230A ILE* 1.3 67.9 + - - +
206C THR 4.2 3.0 + - - -
207C ARG* 3.9 20.8 + - - +
209C SER 5.5 3.4 + - - +
210C GLN* 3.6 22.7 - - + +
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Residues in contact with ILE 230 (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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98A TYR* 4.2 11.2 - - + -
99A PRO 3.0 6.6 + - - +
100A TYR* 2.9 20.7 - - + +
101A ASP* 2.8 24.4 + - - +
147A PHE* 3.8 19.3 - - + -
148A PHE* 3.5 31.0 - - + -
151A LEU* 4.8 1.8 - - + -
181A GLY* 5.9 0.2 - - - -
182A ILE 3.3 9.2 - - - +
183A HIS* 3.8 30.7 - - + -
229A ARG* 1.3 81.9 - - - +
231A SER* 1.3 62.4 + - - +
232A ILE* 4.6 11.4 - - + -
252A ILE* 4.3 15.7 - - + -
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Residues in contact with SER 231 (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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101A ASP* 3.0 30.3 + - - -
103A PRO* 4.3 3.8 - - - -
181A GLY* 3.1 23.6 - - - -
182A ILE* 3.1 11.9 + - - -
184A HIS* 2.8 27.6 + - - -
230A ILE* 1.3 72.8 - - - +
232A ILE* 1.3 60.0 + - - +
233A TYR* 3.6 26.7 - - - -
210C GLN* 4.4 2.3 + - - -
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Residues in contact with ILE 232 (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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71A LEU* 3.8 27.6 - - + -
100A TYR* 3.8 32.5 - - + -
101A ASP 2.8 8.7 + - - +
102A VAL* 3.7 16.8 - - + +
103A PRO* 3.2 22.2 - - - +
108A LEU* 4.0 22.4 - - + -
151A LEU* 3.9 17.5 - - + -
179A ILE* 3.6 23.1 - - + -
180A TRP 3.6 7.2 - - - +
181A GLY* 4.9 2.7 - - - -
230A ILE* 4.6 8.5 - - + -
231A SER* 1.3 74.4 - - - +
233A TYR* 1.3 67.6 + - - +
234A TRP* 5.6 0.2 - - - -
252A ILE* 5.8 0.2 - - + -
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Residues in contact with TYR 233 (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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103A PRO* 3.6 30.8 - - + +
179A ILE* 3.4 7.3 - - - +
180A TRP* 2.8 70.2 + + + +
181A GLY* 4.4 1.1 - - - -
182A ILE* 4.1 8.5 - - + -
184A HIS* 5.7 0.5 + - - -
211A GLN* 4.3 10.1 - - - +
213A ILE* 3.5 39.6 - - + +
231A SER* 3.6 30.9 - - - -
232A ILE* 1.3 77.1 - - - +
234A TRP* 1.3 67.0 + - - +
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Residues in contact with TRP 234 (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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102A VAL* 5.6 1.3 - - + -
103A PRO 5.5 5.6 + - - -
104A ASP* 4.9 9.8 + - - +
107A SER* 4.9 5.0 - - - -
108A LEU* 3.7 31.3 - - + +
111A LEU* 3.6 22.0 - - + -
177A LEU* 3.9 9.9 - - + -
178A TYR 3.3 5.6 - - - -
179A ILE* 3.6 20.6 - - + -
180A TRP* 4.1 0.4 - - - -
211A GLN* 3.7 12.8 + - - +
232A ILE 5.6 0.9 - - - -
233A TYR* 1.3 80.5 - - - +
235A THR* 1.3 65.7 + - - +
236A ILE* 3.7 41.3 - - + -
72F GLU* 5.3 4.5 - - - -
73F VAL 3.3 21.3 - - - -
74F GLU* 4.4 11.0 - - - -
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Residues in contact with THR 235 (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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176A LYS 3.8 0.5 - - - +
177A LEU* 3.6 0.7 - - - -
178A TYR* 2.8 36.3 + - - +
180A TRP* 2.9 23.5 + - - -
204A VAL* 3.5 10.1 - - + +
205A SER* 5.6 1.1 - - - -
206A THR* 4.0 13.5 - - + -
209A SER* 5.2 5.2 - - - +
211A GLN* 3.2 21.9 + - - +
234A TRP* 1.3 71.4 - - - +
236A ILE* 1.3 71.3 + - - +
237A VAL* 3.9 2.3 + - + -
243A LEU* 3.9 24.9 - - + -
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Residues in contact with ILE 236 (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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111A LEU* 4.5 2.2 - - + -
175A ASP* 4.0 29.6 - - + +
176A LYS 3.3 7.9 - - - +
177A LEU* 3.9 10.3 - - + -
206A THR* 4.4 4.7 + - - +
209A SER* 5.6 0.9 + - - -
234A TRP* 3.7 30.6 - - + -
235A THR* 1.3 80.3 - - - +
237A VAL* 1.3 65.1 + - - +
238A LYS* 4.1 11.5 + - + +
260A MET* 3.4 32.5 - - + -
72F GLU* 4.7 9.9 - - - +
73F VAL* 3.7 28.5 - - + +
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Residues in contact with VAL 237 (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 MET 5.1 1.3 - - - +
170A ASN* 2.9 31.9 + - + +
176A LYS* 2.8 25.9 + - + +
178A TYR* 3.6 35.4 - - + +
206A THR* 3.7 19.3 - - + -
235A THR* 4.0 2.5 - - + -
236A ILE* 1.3 77.5 - - - +
238A LYS* 1.3 63.2 + - - +
241A ASP* 3.8 27.1 - - + -
242A VAL* 4.1 11.2 - - - +
243A LEU* 4.0 13.2 - - + +
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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