Contacts of the strand formed by residues 176 - 184 (chain C) 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 LYS 176 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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123C GLU* 2.6 28.5 + - - -
169C PRO 3.2 18.7 + - - -
170C ASN* 3.3 33.4 - - + +
171C ASN 5.4 0.4 - - - +
172C ASP* 4.4 9.2 - - - -
174C PHE* 4.1 4.9 - - + -
175C ASP* 1.3 76.3 - - - +
177C LEU* 1.3 60.4 + - - +
178C TYR* 3.0 28.9 + - + +
235C THR 3.8 0.3 - - - +
236C ILE* 3.3 4.7 - - - +
237C VAL* 2.8 35.5 + - + +
257C TYR* 3.5 44.9 - - + -
258C PHE 3.8 4.5 - - - -
260C MET* 4.8 0.7 - - - -
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Residues in contact with LEU 177 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70C LEU* 4.7 7.2 - - + -
111C LEU* 4.0 13.0 - - + -
112C VAL* 4.8 8.7 - - + -
175C ASP 4.3 0.2 - - - -
176C LYS* 1.3 71.5 - - - +
178C TYR* 1.3 62.5 + - - +
179C ILE* 3.9 14.6 - - + -
234C TRP* 3.9 28.5 - - + -
235C THR 3.6 2.7 - - - +
236C ILE* 3.9 17.9 - - + +
257C TYR* 3.6 1.0 - - - -
258C PHE* 3.0 60.6 + - + +
260C MET* 3.7 33.6 - - + +
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Residues in contact with TYR 178 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123C GLU* 2.8 29.4 + - - -
125C PHE* 4.0 7.2 - + - -
168C MET* 3.5 12.6 + - + +
176C LYS* 3.0 37.0 + - + +
177C LEU* 1.3 74.0 - - - +
179C ILE* 1.4 60.2 + - - +
180C TRP* 3.8 9.5 - - + -
234C TRP* 3.3 4.7 - - - +
235C THR* 2.8 40.2 + - - +
237C VAL* 3.5 34.3 - - + +
243C LEU* 3.7 31.4 - - + -
254C PRO* 4.2 15.9 - - + -
256C GLY 3.2 28.3 - - - -
257C TYR* 3.9 2.9 - - + -
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Residues in contact with ILE 179 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70C LEU* 4.0 11.0 - - + -
71C LEU* 3.6 30.1 - - + -
108C LEU* 3.7 23.1 - - + -
150C ARG* 5.0 2.2 - - + +
151C LEU* 3.5 15.2 - - + +
177C LEU* 3.9 12.0 + - + -
178C TYR* 1.4 71.7 - - - +
180C TRP* 1.3 64.6 + - - +
232C ILE* 3.6 16.6 - - + -
233C TYR 3.4 2.0 - - - +
234C TRP* 3.6 26.0 - - + -
254C PRO* 3.4 18.5 - - - +
256C GLY 5.0 1.4 + - - -
258C PHE* 3.8 30.5 - - + -
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Residues in contact with TRP 180 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151C LEU* 4.1 8.5 - - - -
178C TYR* 3.8 20.9 - - + -
179C ILE* 1.3 75.2 - - - +
181C GLY* 1.3 87.6 + - - +
182C ILE* 5.3 0.4 - - + -
202C VAL* 3.8 21.8 - - + -
204C VAL* 3.4 36.3 - - + +
211C GLN* 3.7 19.1 - - + -
213C ILE* 3.4 31.9 - - + -
232C ILE* 3.6 8.8 - - - +
233C TYR* 2.8 55.9 + + + +
234C TRP 4.1 1.0 - - - -
235C THR* 2.9 23.5 + - - +
243C LEU* 6.1 0.7 - - + -
245C ILE* 5.9 1.1 - - + -
251C LEU* 4.9 2.7 - - + -
252C ILE 3.8 12.1 - - - +
254C PRO* 3.9 17.3 - - + -
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Residues in contact with GLY 181 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180C TRP* 1.3 91.4 - - - +
182C ILE* 1.3 62.3 + - - +
202C VAL* 4.6 0.5 - - - +
230C ILE* 5.9 0.7 - - - -
231C SER 3.2 14.1 - - - -
232C ILE* 4.4 3.6 - - - -
233C TYR* 4.3 1.1 - - - -
251C LEU* 3.7 9.0 - - - +
252C ILE* 3.0 37.5 + - - +
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Residues in contact with ILE 182 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180C TRP* 5.3 0.7 - - + -
181C GLY* 1.3 74.8 - - - +
183C HIS* 1.3 63.2 + - - +
184C HIS* 4.0 18.3 + - + +
201C ARG 4.9 0.4 - - - -
202C VAL* 3.7 18.2 - - + +
213C ILE* 3.5 48.7 - - + +
215C PRO* 3.5 27.4 - - + -
230C ILE* 3.3 4.4 - - - +
231C SER* 3.1 23.2 + - - +
233C TYR* 4.0 13.7 - - + -
250C ASN* 3.2 20.9 - - + +
252C ILE* 4.1 4.5 - - - +
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Residues in contact with HIS 183 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98C TYR* 2.9 29.1 + + - -
153C TRP* 3.8 12.5 - + - -
182C ILE* 1.3 72.4 - - - +
184C HIS* 1.3 59.2 + - - +
185C PRO* 3.6 12.8 - - + +
190C GLU* 3.3 22.8 + - - -
194C LEU* 3.8 14.4 - - + -
195C TYR* 2.8 36.4 + - + +
215C PRO* 3.4 7.8 - - - +
228C SER* 4.0 2.0 - - - -
229C ARG 4.0 5.4 - - - -
230C ILE* 3.7 23.1 - - + -
250C ASN* 2.8 37.7 + - - +
252C ILE* 4.1 8.5 - - + +
329C SIA 3.8 4.2 - - - -
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Residues in contact with HIS 184 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182C ILE* 4.1 13.3 - - + +
183C HIS* 1.3 74.7 - - - +
185C PRO* 1.3 66.1 - - - +
213C ILE* 5.2 2.2 - - + -
214C ILE 4.3 2.7 - - - -
215C PRO* 3.3 12.3 - - + +
216C ASN* 2.7 56.6 + - - +
220C ARG* 3.3 13.6 + - - +
228C SER* 3.4 20.3 - - - -
229C ARG 2.9 24.0 + - - +
231C SER* 2.8 34.4 + - - -
233C TYR* 5.9 0.2 - - - -
210E GLN* 3.7 19.1 + - - -
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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