Contacts of the helix formed by residues 161 - 177 (chain C) in PDB entry 4OGB
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 ASN 161 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153C TYR* 3.5 17.3 - - - -
154C HIS 3.7 10.8 - - - +
157C VAL 2.8 26.2 + - - +
158C ALA 2.9 21.0 + - - -
159C TYR 2.6 12.1 + - - +
160C HIS* 1.3 73.4 - - - +
162C ASN* 1.3 65.4 + - - +
163C ILE* 2.9 19.9 + - - +
164C HIS* 3.2 10.7 + - - +
165C ALA* 3.1 17.5 + - - +
332C TRP* 5.0 1.2 - - - -
335C ARG* 3.6 4.4 - - - +
503C EDO 3.5 30.8 + - - -
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Residues in contact with ASN 162 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115C ASN* 3.1 21.8 + - - -
117C PRO* 3.5 9.1 - - - +
118C LEU* 4.0 5.6 - - + +
150C GLU* 2.7 41.5 + - + +
153C TYR* 3.5 21.7 - - + +
154C HIS 5.3 0.2 - - - +
161C ASN* 1.3 73.5 - - - +
163C ILE* 1.3 55.6 + - - -
165C ALA* 3.2 5.1 + - - +
166C ALA* 2.8 29.6 + - - +
503C EDO 2.9 28.6 + - - -
509C EDO 3.5 16.0 + - - -
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Residues in contact with ILE 163 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106C VAL* 4.1 21.4 - - + +
107C PHE* 3.9 27.4 - - + -
110C ALA* 4.0 16.2 - - + -
115C ASN* 4.6 1.1 - - - +
117C PRO* 4.1 19.3 - - + -
161C ASN* 2.9 10.2 + - - +
162C ASN* 1.3 77.7 - - - +
164C HIS* 1.3 57.7 + - - +
166C ALA* 3.3 2.5 + - - +
167C ASP* 2.9 27.5 + - - +
332C TRP* 3.6 19.5 - - + -
335C ARG* 4.1 10.8 - - - +
503C EDO 3.7 29.8 - - - -
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Residues in contact with HIS 164 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159C TYR* 3.2 58.6 + + - +
160C HIS* 4.3 5.2 - + - -
161C ASN* 3.2 7.3 + - - +
163C ILE* 1.3 79.1 - - - +
165C ALA* 1.3 57.5 + - - +
167C ASP* 3.2 7.2 + - - +
168C VAL* 2.8 41.8 + - + +
200C HIS* 3.2 7.8 + + - -
201C ASP* 3.0 20.9 - - + -
318C ASP* 3.3 13.9 - - - -
321C ASN* 5.1 1.7 + - - -
332C TRP* 3.6 17.5 - - + -
510C ZN 2.2 31.6 - - - -
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Residues in contact with ALA 165 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118C LEU* 4.0 9.2 - - + -
153C TYR* 3.5 40.8 - - + +
161C ASN 3.1 9.1 + - - +
162C ASN 3.5 8.5 - - - +
164C HIS* 1.3 75.1 - - - +
166C ALA* 1.3 65.9 + - - +
168C VAL* 3.3 2.1 + - - +
169C VAL* 2.9 27.9 + - - +
197C SER 4.2 1.6 - - - +
198C ALA 3.9 7.6 - - - +
200C HIS* 4.6 11.2 - - + -
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Residues in contact with ALA 166 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106C VAL* 4.2 2.0 - - + -
117C PRO* 3.9 7.2 - - + -
118C LEU* 3.8 32.2 - - - +
121C ILE* 3.8 27.6 - - + +
162C ASN 2.8 20.0 + - - +
163C ILE 3.5 5.2 - - - +
165C ALA* 1.3 72.0 - - - +
167C ASP* 1.3 57.8 + - - +
169C VAL* 3.3 3.6 + - - +
170C GLN* 2.9 31.9 + - - +
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Residues in contact with ASP 167 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106C VAL* 4.3 15.0 - - + +
163C ILE 2.9 14.3 + - - +
164C HIS* 3.3 11.6 + - - +
166C ALA* 1.3 73.8 - - - +
168C VAL* 1.3 60.4 + - - +
170C GLN* 3.3 8.9 + - - +
171C SER* 2.7 37.2 + - - -
317C ALA 5.3 0.2 - - - +
320C SER* 4.4 3.2 + - - -
321C ASN* 3.4 19.8 + - - -
324C LYS* 3.2 25.8 + - - -
332C TRP* 3.4 31.8 + - + -
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Residues in contact with VAL 168 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164C HIS* 2.8 47.1 + - + +
165C ALA 4.0 1.1 - - - +
167C ASP* 1.3 74.7 - - + +
169C VAL* 1.3 58.0 + - - +
171C SER* 4.4 4.3 - - - -
172C THR* 2.9 35.0 + - - +
197C SER* 3.9 16.6 - - - +
200C HIS* 3.5 27.6 - - + +
314C VAL* 4.4 8.1 - - + +
317C ALA* 3.8 30.0 - - + +
318C ASP* 3.9 9.9 - - - +
321C ASN* 6.4 0.2 - - - +
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Residues in contact with VAL 169 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118C LEU* 4.1 5.2 - - + -
121C ILE* 4.5 3.6 - - + -
122C MET* 3.6 27.4 - - + -
125C ILE* 3.7 19.3 - - + -
165C ALA 2.9 17.6 + - - +
166C ALA* 3.4 11.0 - - - +
168C VAL* 1.3 77.7 - - - +
170C GLN* 1.3 57.8 + - - +
172C THR* 3.3 2.9 + - - -
173C HIS* 3.0 26.7 + - - +
194C ILE* 3.9 11.1 - - + +
197C SER* 3.7 8.5 - - - -
198C ALA* 3.3 41.3 - - + +
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Residues in contact with GLN 170 (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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99C VAL* 2.8 39.3 + - + +
101C LYS 2.9 25.7 + - - +
102C TRP* 5.4 0.9 - - - -
103C GLY 5.0 1.2 + - - -
104C LEU* 3.6 38.0 + - + +
106C VAL* 6.2 0.2 - - - +
121C ILE* 4.0 10.5 - - + -
125C ILE* 3.8 9.6 - - + -
166C ALA 2.9 19.7 + - - +
167C ASP* 3.9 9.1 - - - +
169C VAL* 1.3 73.6 - - - +
171C SER* 1.3 65.2 + - - +
173C HIS* 3.4 2.8 + - - +
174C VAL* 3.1 35.9 + - - +
324C LYS* 4.7 4.3 + - - -
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Residues in contact with SER 171 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102C TRP* 3.5 26.8 - - - -
167C ASP* 2.7 26.0 + - - -
168C VAL* 3.9 3.6 - - - -
170C GLN* 1.3 77.6 + - - +
172C THR* 1.3 64.8 + - - +
174C VAL* 3.3 1.1 + - - -
175C LEU* 3.0 26.9 + - - +
317C ALA* 4.0 13.9 - - - -
320C SER* 3.7 7.0 + - - -
324C LYS* 2.8 26.3 + - - -
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Residues in contact with THR 172 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168C VAL 2.9 16.6 + - - -
169C VAL 3.6 3.6 - - - -
171C SER* 1.3 73.6 - - - +
173C HIS* 1.3 60.1 + - - +
175C LEU* 3.2 7.0 + - - +
176C LEU* 2.8 40.0 + - + +
193C ALA* 3.9 28.7 - - + +
194C ILE* 4.5 3.4 - - + -
197C SER* 2.9 25.2 + - - +
313C MET* 4.3 5.6 - - - -
314C VAL* 3.8 11.7 + - + +
317C ALA* 3.3 17.5 - - - +
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Residues in contact with HIS 173 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99C VAL* 3.4 23.0 + - - +
100C ASN* 2.7 31.0 + - - -
125C ILE* 3.5 35.6 - - + +
128C GLU* 4.0 18.8 - - + +
129C ARG* 2.8 65.4 + - + +
169C VAL 3.0 14.7 + - - +
170C GLN 3.4 7.9 - - - +
172C THR* 1.3 78.3 - - - +
174C VAL* 1.3 62.8 + - + +
176C LEU* 3.6 6.0 + - - -
177C SER* 3.5 7.0 + - - -
194C ILE* 4.8 2.7 - - + -
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Residues in contact with VAL 174 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99C VAL 4.1 1.8 - - - +
100C ASN* 3.7 28.0 - - - +
101C LYS 4.1 4.5 - - - -
102C TRP* 3.7 30.5 - - + +
170C GLN* 3.1 36.1 + - - +
171C SER 3.7 6.7 - - - +
172C THR 3.2 0.2 - - - -
173C HIS* 1.3 75.5 - - - +
175C LEU* 1.3 60.4 + - - +
177C SER* 2.9 27.5 + - - -
178C THR 3.6 2.8 + - - -
513C EDO 4.1 16.8 + - - +
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Residues in contact with LEU 175 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102C TRP* 4.1 11.0 - - + -
171C SER 3.0 20.8 + - - +
172C THR* 3.7 1.6 - - - +
174C VAL* 1.3 76.5 - - - +
176C LEU* 1.3 62.6 + - - +
177C SER 3.1 0.5 + - - -
178C THR* 3.1 21.1 + - - +
181C LEU* 4.0 6.1 - - - +
313C MET* 3.6 45.7 - - + +
316C CYS* 4.2 3.1 - - + -
317C ALA* 4.1 14.8 - - + +
381C TRP* 3.8 25.6 - - + -
384C TRP* 3.6 18.0 - - + +
395C ILE* 4.6 0.7 - - + -
513C EDO 3.5 26.4 + - - +
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Residues in contact with LEU 176 (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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129C ARG* 3.5 20.3 + - - +
172C THR* 2.8 24.2 + - + +
174C VAL 3.2 0.2 - - - -
175C LEU* 1.3 76.4 - - - +
177C SER* 1.3 57.6 + - - +
178C THR 3.2 6.2 + - - +
181C LEU* 4.4 12.5 - - - +
182C GLU* 5.9 0.3 - - - -
185C PHE* 4.2 15.6 - - + -
190C ILE* 4.1 31.2 - - + +
193C ALA* 4.3 4.0 - - + -
194C ILE* 3.9 33.2 - - + -
310C LEU* 4.1 14.8 - - + -
313C MET* 3.5 28.5 - - + -
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Residues in contact with SER 177 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129C ARG* 3.1 20.2 + - - +
173C HIS* 3.5 7.4 + - - -
174C VAL* 2.9 15.3 + - - -
176C LEU* 1.3 74.5 - - - +
178C THR* 1.3 66.9 + - - +
179C PRO* 3.3 6.4 - - - +
513C EDO 4.7 0.7 - - - -
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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