Contacts of the helix formed by residues 202 - 220 (chain B) in PDB entry 3J41
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 TRP 202 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127B VAL* 4.4 11.7 - - + +
131B THR* 4.4 8.1 + - - +
198B PHE 5.0 0.2 + - - -
200B ASN* 3.0 3.3 + - - +
201B HIS* 1.3 76.1 - - - +
203B VAL* 1.3 76.5 + - + +
205B TRP* 3.3 6.9 + - + +
206B VAL* 3.0 65.0 + - + +
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Residues in contact with VAL 203 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121B LEU* 4.4 15.0 - - + -
127B VAL* 3.6 36.8 - - + +
130B ALA* 3.7 31.4 - - + +
131B THR* 3.6 14.3 + - - +
134B GLU* 3.9 10.4 - - + +
200B ASN* 2.9 19.0 + - + +
202B TRP* 1.3 81.5 - - + +
204B TYR* 1.3 64.9 + - + +
206B VAL* 4.8 0.7 - - - -
207B GLY* 3.0 26.9 + - - -
208B PRO* 3.6 4.0 - - - +
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Residues in contact with TYR 204 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119B ASN* 3.4 40.8 - - + -
120B THR 3.1 19.9 - - - -
121B LEU* 3.1 29.0 - - + +
134B GLU* 3.8 20.6 - - + -
179B THR* 2.9 26.8 + - - -
182B GLY* 4.0 9.4 - - - -
185B PRO* 3.5 21.3 - - - +
188B SER* 3.2 26.9 + - - +
199B THR 5.2 1.1 - - - -
200B ASN* 3.7 15.5 - - + -
201B HIS* 2.9 21.9 + + + +
203B VAL* 1.3 77.0 - - + +
205B TRP* 1.3 57.7 + - - +
208B PRO* 3.6 17.2 - - - +
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Residues in contact with TRP 205 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69B PRO* 4.6 0.9 - - + -
90B MET* 4.4 21.1 - - + -
94B LEU* 3.9 35.9 - - + -
185B PRO* 3.6 32.2 + - + -
189B PHE* 4.3 14.6 - + + -
201B HIS* 2.9 46.7 + + - +
202B TRP* 3.3 8.0 + - - +
203B VAL 3.2 0.4 - - - -
204B TYR* 1.3 80.2 - - - +
206B VAL* 1.3 65.6 + - + +
207B GLY 3.5 0.4 - - - -
208B PRO* 3.7 1.5 - - - +
209B VAL* 2.9 46.8 + - + +
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Residues in contact with VAL 206 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131B THR* 3.6 17.9 - - + -
202B TRP* 3.0 71.1 + - + +
203B VAL 4.3 0.9 - - - +
205B TRP* 1.3 77.3 - - + +
207B GLY* 1.3 61.0 + - - +
209B VAL* 3.9 3.3 - - - +
210B ILE* 2.8 58.8 + - + +
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Residues in contact with GLY 207 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131B THR* 3.7 12.7 - - - +
134B GLU* 3.8 10.1 - - - -
135B ILE* 3.4 24.2 - - - +
203B VAL 3.0 13.5 + - - -
206B VAL* 1.3 78.7 - - - +
208B PRO* 1.3 55.8 - - - +
211B GLY* 2.6 34.7 + - - -
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Residues in contact with PRO 208 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70B ALA* 3.6 19.3 - - + -
134B GLU* 3.6 22.9 - - + +
138B THR* 3.0 22.3 - - + +
183B MET* 3.9 11.9 - - - +
184B ASN 4.0 2.2 - - - +
185B PRO* 4.1 9.2 - - + -
203B VAL 3.6 11.9 - - - +
204B TYR* 3.6 20.6 - - - +
205B TRP 3.7 2.7 - - - +
207B GLY* 1.3 89.0 - - - +
209B VAL* 1.3 53.3 + - - +
212B ALA* 2.5 38.8 + - - +
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Residues in contact with VAL 209 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69B PRO* 5.8 0.9 - - + -
70B ALA* 4.4 10.1 - - + +
73B PHE* 3.6 36.6 - - + -
185B PRO* 4.6 13.2 - - + -
205B TRP* 2.9 37.0 + - + +
206B VAL* 3.9 4.0 - - - +
208B PRO* 1.3 74.9 - - - +
210B ILE* 1.3 63.8 + - + +
212B ALA* 3.6 5.4 - - - +
213B GLY* 2.9 23.6 + - - -
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Residues in contact with ILE 210 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131B THR* 5.3 0.9 - - + -
135B ILE* 3.7 25.4 - - + -
206B VAL* 2.8 44.5 + - + +
207B GLY 3.9 1.8 - - - +
209B VAL* 1.3 76.7 - - + +
211B GLY* 1.3 58.2 - - - +
213B GLY* 3.0 3.7 + - - +
214B LEU* 2.8 49.4 + - + +
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Residues in contact with GLY 211 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135B ILE* 3.3 33.8 - - - +
138B THR* 4.2 0.7 - - - -
139B LEU* 3.5 19.0 - - - -
207B GLY 2.6 18.7 + - - -
208B PRO 3.7 0.9 - - - -
210B ILE* 1.3 74.8 - - - +
212B ALA* 1.3 56.2 + - - +
214B LEU* 3.2 3.1 + - - +
215B GLY 2.9 24.9 + - - -
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Residues in contact with ALA 212 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70B ALA* 3.0 33.2 - - + +
73B PHE* 4.5 1.3 - - + -
74B ALA* 3.7 10.2 - - + +
138B THR* 3.7 2.1 - - + +
142B VAL* 3.5 25.1 - - + +
208B PRO 2.5 23.0 + - - +
209B VAL* 3.6 4.7 - - - +
211B GLY* 1.3 72.1 - - - +
213B GLY* 1.3 63.0 + - - +
215B GLY 3.4 0.2 + - - -
216B SER* 3.0 25.1 + - - -
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Residues in contact with GLY 213 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73B PHE* 4.1 15.2 - - - -
77B VAL* 4.7 5.2 - - - -
209B VAL 2.9 15.2 + - - -
210B ILE* 3.0 4.7 + - - -
212B ALA* 1.3 78.0 - - - +
214B LEU* 1.3 59.6 + - - +
216B SER* 3.5 4.5 + - - -
217B LEU* 2.9 40.2 + - - +
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Residues in contact with LEU 214 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135B ILE* 3.9 18.6 - - + -
139B LEU* 3.8 18.6 - - + -
210B ILE* 2.8 43.1 + - + +
211B GLY 3.7 3.8 - - - +
213B GLY* 1.3 71.9 - - - +
215B GLY* 1.3 56.6 + - - +
217B LEU* 3.6 15.4 - - + +
218B LEU* 2.6 37.6 + - - +
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Residues in contact with GLY 215 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139B LEU* 3.2 28.0 - - - +
142B VAL* 4.1 9.6 - - - -
143B LEU* 4.6 7.3 - - - +
146B PHE* 5.0 0.6 - - - -
211B GLY 2.9 14.0 + - - -
212B ALA 3.8 1.3 - - - -
213B GLY 3.3 0.2 - - - -
214B LEU* 1.3 74.7 - - - +
216B SER* 1.3 63.6 + - - +
218B LEU* 3.8 1.6 - - - +
219B TYR* 3.0 27.5 + - - +
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Residues in contact with SER 216 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74B ALA 3.0 26.4 + - - -
77B VAL* 3.5 10.9 + - - +
78B GLY* 3.5 13.0 - - - -
142B VAL* 3.9 2.0 - - - +
146B PHE* 3.3 25.8 - - - -
212B ALA 3.0 16.7 + - - -
213B GLY 3.7 4.5 - - - -
215B GLY* 1.3 75.7 - - - +
217B LEU* 1.3 59.4 + - - +
219B TYR* 3.9 0.2 - - - +
220B ASP* 2.9 37.2 + - - +
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Residues in contact with LEU 217 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77B VAL* 4.6 20.4 - - + +
213B GLY* 2.9 26.7 + - - +
214B LEU* 3.6 16.4 - - + +
216B SER* 1.3 78.1 - - - +
218B LEU* 1.3 69.5 + - - +
219B TYR 2.8 2.1 + - - -
220B ASP* 2.9 21.0 + - + +
221B PHE* 5.7 10.3 - - + -
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Residues in contact with LEU 218 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139B LEU* 4.2 15.0 - - + -
143B LEU* 4.2 13.5 - - + -
214B LEU 2.6 23.0 + - - +
215B GLY* 3.8 3.8 - - - +
217B LEU* 1.3 72.7 - - - +
219B TYR* 1.3 63.1 + - - +
220B ASP 4.9 0.3 - - - +
18C PHE* 3.5 47.3 - - + -
22C PHE* 4.1 27.8 - - + -
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Residues in contact with TYR 219 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143B LEU* 3.7 24.0 - - + -
146B PHE* 3.8 34.8 - + + -
147B ALA* 3.5 26.1 - - + -
150B ASP* 2.4 37.0 + - - +
152B ARG* 4.2 11.0 - - - -
215B GLY 3.0 17.7 + - - +
216B SER 3.9 2.5 - - - +
217B LEU 2.8 3.0 + - - -
218B LEU* 1.3 76.9 - - - +
220B ASP* 1.3 71.4 + - - +
221B PHE 4.9 1.1 - - - +
222B LEU* 5.0 4.7 - - + -
58C ALA 4.0 4.9 - - - -
61C HIS* 3.1 26.8 - + - -
62C ILE* 4.5 11.7 - - + -
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Residues in contact with ASP 220 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B VAL 4.7 0.2 - - - +
78B GLY* 3.5 25.1 - - - +
80B GLN* 5.1 2.3 - - - +
146B PHE* 3.5 20.0 - - - -
216B SER* 2.9 28.2 + - - +
217B LEU* 2.9 12.5 + - + +
218B LEU 4.9 0.3 - - - +
219B TYR* 1.3 87.4 - - - +
221B PHE* 1.3 99.6 + - + +
222B LEU* 4.7 4.7 + - - +
11C ARG* 5.9 1.6 + - - -
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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
------------------------------------------------------------
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