Contacts of the helix formed by residues 168 - 184 (chain A) in PDB entry 5BUG
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 ILE 168 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93A HIS* 3.6 56.5 - - + +
166A VAL* 3.7 1.2 - - - +
167A THR* 1.3 85.8 - - - +
169A PRO* 1.3 70.8 - - + +
170A SER* 4.0 4.3 - - - +
171A GLN* 3.0 37.0 + - + +
172A ARG* 3.0 12.0 + - - +
272A HIS* 5.6 0.4 - - + -
326A ASP* 3.6 30.1 - - + +
330A LYS* 6.5 0.9 - - - -
401A TLA 4.9 0.7 - - - +
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Residues in contact with PRO 169 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167A THR 3.3 8.5 - - - +
168A ILE* 1.3 82.3 - - + +
170A SER* 1.3 55.7 + - - +
172A ARG* 3.3 13.0 + - + +
173A ARG* 2.8 34.3 + - - +
323A ASN 3.6 18.4 - - - +
324A ASP* 3.4 27.4 - - - +
325A LEU 3.7 14.1 - - - +
326A ASP* 3.3 16.2 - - - +
329A ASN* 3.7 19.5 - - - +
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Residues in contact with SER 170 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94A ASN* 5.6 0.2 - - - -
95A PRO* 3.7 22.8 - - - +
168A ILE* 3.2 2.7 - - - -
169A PRO* 1.3 71.1 - - - +
171A GLN* 1.3 66.7 - - - +
173A ARG* 3.3 18.1 + - - +
174A TYR* 3.2 26.5 - - - -
273A PHE* 3.8 0.3 - - - -
274A TRP* 3.1 30.3 + - - -
326A ASP* 2.8 34.8 + - - -
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Residues in contact with GLN 171 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93A HIS* 3.7 7.9 - - - +
94A ASN* 3.0 43.1 + - - +
95A PRO* 4.3 4.7 - - - -
129A GLY* 3.3 26.4 - - - -
130A ARG* 3.9 20.0 - - - +
133A VAL* 3.6 14.4 - - + +
166A VAL* 3.3 16.8 - - + +
167A THR 5.0 0.2 + - - -
168A ILE* 3.0 34.9 + - + +
170A SER* 1.3 77.2 - - - +
172A ARG* 1.3 62.5 + - - +
174A TYR* 3.4 10.2 + - - +
175A VAL* 3.6 15.6 + - - +
401A TLA 4.2 3.5 + - - +
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Residues in contact with ARG 172 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149A GLN* 4.9 14.3 - - - +
152A LEU* 3.8 42.0 + - + +
153A ASP* 4.8 9.1 + - - -
166A VAL* 2.9 48.6 + - + +
167A THR* 4.2 9.8 - - - +
168A ILE 3.0 13.0 + - - +
169A PRO* 3.6 12.3 - - + +
171A GLN* 1.3 73.9 - - - +
173A ARG* 1.3 66.4 + - - +
175A VAL* 3.3 9.7 + - - +
176A TYR* 3.2 39.4 + - + -
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Residues in contact with ARG 173 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169A PRO* 2.8 20.9 + - - +
170A SER* 3.4 32.0 + - - +
171A GLN 3.2 0.4 - - - -
172A ARG* 1.3 77.6 - - - +
174A TYR* 1.3 58.7 + - + +
176A TYR* 3.2 12.0 + - + +
177A TYR* 2.8 64.2 + - + -
273A PHE* 4.3 3.8 - - - +
274A TRP 2.8 36.2 + - - +
275A VAL* 4.3 4.7 - - - +
318A LEU* 5.9 1.1 - - - +
320A LEU* 3.5 20.5 - - - +
324A ASP* 3.0 44.5 + - - +
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Residues in contact with TYR 174 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95A PRO* 3.4 27.4 - - + -
96A PRO* 3.2 35.2 - - + -
98A LEU* 4.0 22.9 - - + -
101A ILE* 4.0 13.3 - - + +
133A VAL* 4.7 1.3 - - + -
170A SER 3.2 14.5 + - - -
171A GLN 3.9 4.9 - - - +
172A ARG 3.2 0.8 - - - -
173A ARG* 1.3 75.1 - - + +
175A VAL* 1.3 61.9 + - - +
177A TYR* 3.5 29.1 - + - +
178A TYR* 3.1 25.6 + - - +
252A ASP* 2.7 36.3 + - - +
274A TRP* 4.1 22.7 - + + -
275A VAL 3.8 13.0 + - - -
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Residues in contact with VAL 175 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133A VAL* 3.8 34.1 - - + +
136A CYS* 3.9 17.9 - - + -
137A ALA* 4.4 5.8 - - - +
140A LEU* 3.7 23.9 - - + +
148A ALA* 4.2 9.9 - - + +
152A LEU* 4.3 22.4 - - + -
171A GLN 3.6 15.0 - - - +
172A ARG 3.3 6.9 + - - +
173A ARG 3.3 0.4 - - - -
174A TYR* 1.3 77.8 - - - +
176A TYR* 1.3 58.2 + - - +
178A TYR* 3.4 5.3 + - - +
179A SER* 3.0 27.5 + - - -
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Residues in contact with TYR 176 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148A ALA* 3.8 22.4 - - + -
149A GLN* 3.5 32.8 + - + +
152A LEU* 4.1 17.7 - - + -
172A ARG* 3.2 39.4 + - + -
173A ARG* 3.2 11.8 + - + +
175A VAL* 1.3 73.8 - - - +
177A TYR* 1.3 62.1 + - + +
179A SER* 3.4 3.2 + - - -
180A TYR* 2.9 29.6 + - - +
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Residues in contact with TYR 177 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98A LEU* 4.0 7.4 - - + -
173A ARG* 2.8 41.8 + - + -
174A TYR* 3.5 43.5 - + - +
176A TYR* 1.3 76.2 - - + +
178A TYR* 1.3 61.9 + - - +
180A TYR* 3.1 6.1 + - + +
181A LEU* 3.0 20.3 + - - +
275A VAL* 3.7 7.8 - - - +
276A ASN* 3.1 43.0 + - + -
279A PHE* 3.3 62.6 - + + +
280A ILE* 5.5 0.2 - - - +
318A LEU* 5.2 2.8 - - - +
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Residues in contact with TYR 178 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98A LEU* 4.8 4.4 - - + +
101A ILE* 3.5 38.8 - - + -
102A LYS* 3.6 31.7 - - + +
105A CYS* 3.8 6.1 - - - +
137A ALA* 3.6 30.7 - - + -
140A LEU* 5.1 1.1 - - + -
141A HIS* 2.7 29.8 + - - -
174A TYR 3.1 13.7 + - - +
175A VAL 3.4 4.0 + - - +
177A TYR* 1.3 79.0 - - - +
179A SER* 1.3 62.0 + - - +
181A LEU* 3.2 25.2 + - + +
182A LEU* 3.0 55.0 + - + +
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Residues in contact with SER 179 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140A LEU* 3.8 20.5 - - - +
146A LEU 4.4 7.4 + - - -
147A LYS* 4.7 0.5 - - - -
148A ALA* 4.0 20.4 + - - -
175A VAL 3.0 18.4 + - - -
176A TYR* 3.5 7.4 - - - -
178A TYR* 1.3 78.8 - - - +
180A TYR* 1.3 55.9 + - - +
182A LEU* 3.4 11.7 + - - +
183A LYS* 2.9 33.5 + - - +
43C GLU* 5.0 2.6 - - - +
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Residues in contact with TYR 180 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176A TYR 2.9 14.2 + - - +
177A TYR* 3.1 10.3 + - + +
179A SER* 1.3 73.3 - - - +
181A LEU* 1.3 65.3 + - - +
183A LYS* 4.5 7.0 - - + -
184A ASN* 3.0 51.7 + - - +
186A LEU* 3.7 26.1 - - + +
278A PHE* 4.9 4.3 - + - -
279A PHE* 3.7 29.2 - + + -
282A GLY 4.4 15.5 + - - -
283A PRO* 5.6 9.8 - - + +
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Residues in contact with LEU 181 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98A LEU* 3.8 27.8 - - + -
177A TYR 3.0 15.7 + - - +
178A TYR* 3.2 29.4 + - + +
180A TYR* 1.3 77.2 - - - +
182A LEU* 1.3 59.9 + - + +
185A HIS* 3.2 2.3 + - - -
186A LEU* 3.0 53.6 + - + +
188A TYR* 4.1 16.6 - - + +
278A PHE* 3.8 31.0 - - + -
279A PHE* 3.9 11.2 - - + -
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Residues in contact with LEU 182 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140A LEU* 3.7 16.2 - - + +
141A HIS* 3.6 44.4 - - + +
178A TYR* 3.0 51.5 + - + +
179A SER* 3.8 5.2 - - - +
180A TYR 3.3 0.2 - - - -
181A LEU* 1.3 75.5 - - + +
183A LYS* 1.3 64.8 + - - +
185A HIS* 3.2 14.3 + - - +
42C LEU* 4.8 11.4 + - - +
43C GLU* 4.4 14.8 - - + +
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Residues in contact with LYS 183 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146A LEU 5.8 1.1 - - - +
147A LYS* 5.4 9.5 - - - +
179A SER* 2.9 21.7 + - - +
180A TYR* 4.1 8.5 - - + +
182A LEU* 1.3 76.7 - - - +
184A ASN* 1.3 73.1 + - - +
185A HIS* 3.8 0.5 + - - +
42C LEU* 4.1 9.2 - - - +
43C GLU 3.0 25.7 + - - +
44C GLY* 3.1 24.1 + - - +
45C VAL* 3.4 31.4 - - + +
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Residues in contact with ASN 184 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180A TYR* 3.0 53.3 + - - +
183A LYS* 1.3 95.4 + - - +
185A HIS* 1.3 70.7 + - - +
186A LEU* 3.2 25.5 + - + +
45C VAL* 5.2 3.4 - - - +
74C ARG* 5.0 3.1 + - - -
125C LYS* 5.6 2.8 + - - -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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