Contacts of the helix formed by residues 151 - 163 (chain L) in PDB entry 2X5V
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 LEU 151 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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62L PHE* 3.5 36.1 + - + +
150L ILE* 1.3 79.1 - - + +
152L SER* 1.3 63.4 + - - +
153L HIS 3.5 0.9 - - - -
154L LEU* 3.3 30.5 - - + +
155L ASP* 3.7 9.2 + - - +
1275L BCB 4.1 17.0 - - - -
195M TYR 4.5 8.3 - - - +
196M TYR* 4.2 15.6 + - + -
296M CYS* 5.3 4.3 - - - -
301M ALA* 3.5 40.8 - - + +
302M ALA* 4.0 5.6 - - - +
303M PRO* 3.8 13.2 - - + -
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Residues in contact with SER 152 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17C LEU* 5.4 0.3 - - - +
62L PHE 4.6 1.0 + - - -
64L ILE 4.7 1.1 - - - -
65L SER* 2.7 37.4 + - - -
147L PRO* 3.7 10.7 - - - +
149L GLY* 3.0 16.2 + - - -
150L ILE 3.5 0.4 - - - -
151L LEU* 1.3 75.4 - - - +
153L HIS* 1.3 64.8 + - - +
154L LEU 3.1 2.0 - - - -
155L ASP* 2.9 24.9 + - - +
156L TRP 3.3 4.3 + - - -
303M PRO* 4.1 8.8 - - - +
305M TYR* 3.3 24.9 + - - -
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Residues in contact with HIS 153 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146L PHE* 4.1 10.3 - - + -
147L PRO* 3.2 30.3 - - - +
149L GLY 2.7 22.4 + - - +
150L ILE* 3.1 21.8 + - - -
152L SER* 1.3 80.4 + - - +
154L LEU* 1.3 69.6 + - + +
156L TRP* 3.5 5.9 - - - +
157L VAL* 3.1 27.2 + - - +
1275L BCB 2.5 84.9 + + + -
1276L BPB 4.1 10.0 - - + +
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Residues in contact with LEU 154 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150L ILE 3.9 5.6 - - - +
151L LEU* 3.3 21.1 - - + +
153L HIS* 1.3 95.4 - - + +
155L ASP* 1.3 61.6 + - - +
157L VAL* 2.9 12.3 + - - +
158L ASN* 2.9 28.5 + - - +
1275L BCB 3.5 62.4 - - + +
195M TYR* 3.4 46.8 - - + +
196M TYR* 5.8 0.9 - - + -
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Residues in contact with ASP 155 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17C LEU* 4.0 11.9 - - + -
251C GLN* 2.9 37.9 + - + +
151L LEU 4.0 4.6 - - - +
152L SER 2.9 11.4 + - - +
154L LEU* 1.3 79.3 - - - +
156L TRP* 1.3 59.6 + - - +
158L ASN* 3.9 7.0 - - - +
159L ASN* 2.7 36.0 + - - +
193M ASN* 4.6 1.4 + - - -
195M TYR* 5.4 0.3 - - - +
196M TYR* 2.7 31.4 + - - -
303M PRO* 3.7 0.7 - - - +
305M TYR* 2.7 23.9 + - - +
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Residues in contact with TRP 156 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16C GLY 3.2 21.3 - - - +
17C LEU* 3.7 8.7 - - - +
18C SER* 3.5 27.1 - - - +
131L LEU* 4.1 21.1 - - + -
135L ARG* 4.9 2.2 - - - -
144L HIS 3.3 23.2 + - - -
145L ALA* 3.2 17.2 + - - -
146L PHE* 3.3 29.8 - + + -
147L PRO* 3.4 21.5 - - + -
152L SER 3.3 2.8 + - - -
153L HIS 3.5 4.5 - - - +
154L LEU 3.1 0.4 - - - -
155L ASP* 1.3 76.5 - - - +
157L VAL* 1.3 87.9 + - + +
159L ASN* 3.1 4.7 + - - +
160L PHE* 2.7 71.5 + + + +
1275L BCB 4.3 14.6 - - + -
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Residues in contact with VAL 157 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153L HIS 3.1 17.9 - - - +
154L LEU* 2.9 8.9 + - - +
156L TRP* 1.3 93.9 - - + +
158L ASN* 1.3 56.4 + - - +
160L PHE* 3.6 4.6 - - - +
161L GLY* 3.0 22.3 + - - -
1274L BCB 3.4 36.7 - - + +
1275L BCB 3.9 37.5 - - + -
195M TYR* 3.7 16.6 - - + +
1325M BCB 3.9 7.9 - - - +
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Residues in contact with ASN 158 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250C ALA* 2.8 39.3 + - + +
251C GLN* 3.6 0.6 - - - +
253C PHE* 4.8 0.2 - - - -
154L LEU 2.9 11.8 + - - +
155L ASP* 3.9 9.4 - - - +
156L TRP 3.1 0.2 + - - -
157L VAL* 1.3 74.5 - - - +
159L ASN* 1.3 58.1 + - - +
161L GLY 3.3 1.2 + - - -
162L TYR* 2.9 61.8 + - - -
1274L BCB 3.5 4.5 - - - +
193M ASN* 3.3 22.7 + - - +
195M TYR* 3.4 30.5 - - + -
1325M BCB 5.4 1.0 - - - +
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Residues in contact with ASN 159 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17C LEU* 3.0 32.4 + - - +
18C SER 3.4 10.3 - - - +
19C MET* 3.6 12.8 - - - +
245C THR* 3.3 16.8 - - + +
249C ASN* 3.2 18.2 + - - -
250C ALA* 2.9 31.7 + - - +
251C GLN 4.6 1.6 - - - +
155L ASP 2.7 21.5 + - - +
156L TRP 3.1 1.0 + - - -
158L ASN* 1.3 77.3 - - - +
160L PHE* 1.3 62.9 + - - +
162L TYR 4.5 0.4 - - - +
163L GLN* 3.1 29.1 + - - +
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Residues in contact with PHE 160 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18C SER* 3.3 15.8 + - - +
131L LEU* 4.7 0.2 - - + -
135L ARG* 3.4 43.3 - - - -
156L TRP* 2.7 56.4 + + + +
157L VAL* 3.6 6.7 - - - +
159L ASN* 1.3 70.3 - - - +
161L GLY* 1.3 62.6 + - - +
163L GLN* 3.3 25.1 + - - +
164L TYR* 3.4 20.2 - + - -
167L TRP* 3.9 13.9 - + - -
248L THR* 3.6 30.5 - - + -
251L SER 4.3 1.8 - - - -
1274L BCB 3.1 19.7 - - + -
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Residues in contact with GLY 161 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157L VAL 3.0 11.6 + - - -
159L ASN 3.3 0.2 - - - -
160L PHE* 1.3 76.9 - - - +
162L TYR* 1.3 59.6 + - - +
163L GLN 3.2 1.3 + - - -
164L TYR* 3.3 12.8 + - - -
165L LEU 3.8 4.0 + - - -
167L TRP* 3.7 37.6 + - - +
1274L BCB 3.6 23.3 - - - +
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Residues in contact with TYR 162 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230C PHE* 4.9 0.7 - + - -
243C ASN* 4.0 0.2 - - - +
244C CYS* 3.5 32.4 + - + -
245C THR* 5.3 2.9 - - + -
250C ALA* 3.6 9.6 - - + -
253C PHE* 3.5 40.5 - + - -
1335C HEC 3.9 19.1 - - + -
158L ASN* 2.9 46.8 + - - +
159L ASN* 3.9 3.4 - - - +
161L GLY* 1.3 72.1 - - - +
163L GLN* 1.3 60.1 + - - +
164L TYR 3.1 2.7 - - - -
165L LEU* 3.1 32.4 + - - +
166L ASN* 5.8 1.8 - - - -
1274L BCB 4.0 8.5 - - + -
185M THR* 3.8 26.7 + - + +
188M SER* 5.3 1.0 + - - -
189M ILE* 4.2 7.1 - - - +
193M ASN* 5.9 0.2 - - - -
1325M BCB 3.8 17.9 - - + +
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Residues in contact with GLN 163 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9C THR* 6.3 0.6 - - - -
10C THR 5.5 0.2 + - - -
18C SER* 2.7 38.7 + - - +
19C MET 4.4 0.2 - - - -
20C GLY* 3.0 25.0 + - - +
21C GLU 5.1 0.2 + - - -
22C VAL* 3.9 19.3 - - + +
243C ASN* 3.1 40.4 + - - +
245C THR* 3.6 5.4 - - - +
135L ARG* 5.0 4.2 + - - +
144L HIS* 5.8 5.5 + - - -
159L ASN 3.1 16.1 + - - +
160L PHE* 3.3 22.4 - - - +
161L GLY 3.2 0.6 - - - -
162L TYR* 1.3 76.8 - - - +
164L TYR* 1.3 71.0 + - + +
165L LEU* 3.4 1.8 - - - +
256L THR 5.2 2.4 - - - +
257L ARG 4.9 1.7 - - - +
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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
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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