Contacts of the helix formed by residues 285 - 303 (chain B) in PDB entry 3CTP
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 PRO 285 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154B SER* 3.6 15.9 - - - +
283B ASN* 3.8 15.3 - - - +
284B GLN* 1.4 78.0 - - - +
286B ILE* 1.3 66.1 + - - +
287B GLU 3.2 2.9 - - - -
288B ALA* 3.1 14.4 + - + +
289B LEU* 2.8 21.8 + - + +
313B MET* 3.5 24.7 - - + -
314B GLU 3.3 28.5 - - - +
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Residues in contact with ILE 286 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74B PHE* 3.6 37.2 - - + -
77B GLN* 3.8 35.4 - - + +
78B MET* 3.7 27.8 - - + +
81B VAL* 3.8 30.3 - - + -
267B ASP 5.3 0.2 - - - +
268B ASN 5.0 7.9 - - - +
284B GLN 2.9 14.8 + - - +
285B PRO* 1.3 72.3 - - - +
287B GLU* 1.3 65.6 + - + +
289B LEU* 3.7 1.6 - - - +
290B ALA* 2.9 23.4 + - + +
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Residues in contact with GLU 287 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81B VAL* 3.7 26.1 - - + +
85B TYR* 2.6 42.4 + - - +
285B PRO 3.2 1.0 - - - -
286B ILE* 1.3 78.1 - - + +
288B ALA* 1.3 57.2 + - - +
291B TYR* 2.9 31.9 + - - +
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Residues in contact with ALA 288 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285B PRO* 3.1 23.2 + - + +
287B GLU* 1.3 76.4 - - - +
289B LEU* 1.3 65.3 + - - +
291B TYR* 3.8 6.5 - - - +
292B THR* 2.8 31.6 + - - +
313B MET* 4.0 19.3 - - + -
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Residues in contact with LEU 289 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74B PHE* 4.4 1.3 - - + -
78B MET* 4.0 25.1 - - + -
141B PHE* 4.1 12.3 - - + -
152B ILE* 3.8 13.6 - - + +
153B SER 3.8 24.7 - - - +
154B SER* 3.5 19.5 - - - +
284B GLN* 4.0 15.5 - - + +
285B PRO* 2.8 26.4 + - + +
286B ILE* 3.7 3.8 - - - +
288B ALA* 1.3 77.2 - - - +
290B ALA* 1.3 58.2 + - - +
292B THR* 3.3 3.8 + - - -
293B ILE* 2.9 36.5 + - + +
313B MET* 3.7 22.9 - - + +
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Residues in contact with ALA 290 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78B MET* 4.8 2.2 - - + +
81B VAL* 3.7 25.6 - - + -
82B ILE* 3.7 31.9 - - + +
85B TYR* 3.8 5.8 - - + -
286B ILE* 2.9 19.0 + - + +
287B GLU 3.9 0.2 - - - +
289B LEU* 1.3 72.9 - - - +
291B TYR* 1.3 68.2 + - - +
293B ILE* 3.4 3.6 + - - +
294B ILE* 3.1 29.3 + - - +
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Residues in contact with TYR 291 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85B TYR* 3.7 38.6 - + + +
287B GLU 2.9 18.8 + - - +
288B ALA* 3.8 6.5 - - - +
290B ALA* 1.3 75.9 - - - +
292B THR* 1.3 69.9 + - - +
294B ILE* 3.9 1.6 - - - +
295B GLU* 2.8 73.6 + - + +
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Residues in contact with THR 292 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152B ILE* 4.2 13.7 - - + -
288B ALA* 2.8 22.4 + - - +
289B LEU 3.7 3.1 - - - -
291B TYR* 1.3 86.2 - - - +
293B ILE* 1.3 67.7 + - - +
295B GLU* 3.8 3.3 - - - +
296B LEU* 3.0 46.7 + - + +
311B TYR* 3.7 22.4 - - + -
313B MET* 3.9 16.0 - - + -
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Residues in contact with ILE 293 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78B MET* 4.3 14.1 - - - -
82B ILE* 4.2 20.0 - - + -
121B ILE* 3.7 41.1 - - + -
139B VAL* 3.9 10.2 - - + +
140B ALA 6.0 0.4 - - - -
141B PHE* 4.3 23.1 - - + -
152B ILE* 4.0 30.3 - - + -
289B LEU 2.9 27.8 + - - +
290B ALA* 3.8 4.5 - - - +
292B THR* 1.3 75.2 - - - +
294B ILE* 1.3 60.9 + - + +
296B LEU* 4.0 0.3 - - - +
297B LEU* 2.9 28.8 + - - +
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Residues in contact with ILE 294 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63B ILE* 4.3 13.7 - - + -
82B ILE* 3.9 26.5 - - + +
85B TYR* 3.7 36.3 - - + +
86B ALA* 4.0 19.7 - - + +
89B LYS* 3.8 21.1 - - + -
121B ILE* 4.1 14.4 - - + -
290B ALA 3.1 17.5 + - - +
291B TYR 3.9 2.0 - - - +
293B ILE* 1.3 74.9 - - + +
295B GLU* 1.3 66.9 + - - +
297B LEU* 3.9 3.9 - - + +
298B ILE* 3.0 29.0 + - + +
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Residues in contact with GLU 295 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89B LYS* 2.8 38.8 + - - +
291B TYR* 2.8 69.7 + - + +
292B THR* 3.8 5.6 - - - +
294B ILE* 1.3 74.9 - - - +
296B LEU* 1.3 65.5 + - + +
298B ILE* 3.5 5.5 + - - +
299B LYS* 3.2 36.0 + - - +
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Residues in contact with LEU 296 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139B VAL* 4.3 7.6 - - + -
150B ILE* 3.9 22.7 - - + -
152B ILE* 3.9 7.0 - - + -
292B THR* 3.0 41.1 + - + +
293B ILE* 4.0 2.5 - - - +
295B GLU* 1.3 75.9 - - + +
297B LEU* 1.3 66.7 + - - +
299B LYS* 3.1 26.6 + - + +
300B ILE* 3.1 17.0 + - - +
306B VAL* 3.9 19.3 - - + -
311B TYR* 3.6 47.6 - - + +
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Residues in contact with LEU 297 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63B ILE* 3.7 43.1 - - + -
119B GLY* 4.3 1.6 - - - -
120B ILE 4.0 13.5 - - - +
121B ILE* 3.8 17.5 - - + -
137B PRO* 3.8 37.0 - - + +
139B VAL* 3.9 19.6 - - + +
293B ILE 2.9 19.2 + - - +
294B ILE* 3.9 5.6 - - + +
296B LEU* 1.3 77.2 - - - +
298B ILE* 1.3 58.7 + - + +
300B ILE* 3.2 5.3 + - + +
301B ILE* 2.8 39.6 + - + +
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Residues in contact with ILE 298 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63B ILE* 4.7 6.5 - - + -
89B LYS* 4.0 32.8 - - + +
91B TYR* 3.2 44.6 - - + +
294B ILE* 3.0 24.1 + - + +
295B GLU* 3.8 5.6 - - - +
297B LEU* 1.3 75.9 - - + +
299B LYS* 1.3 58.1 + - + +
301B ILE* 3.6 13.6 - - + +
302B ASN* 2.9 49.9 + - - +
304B GLU* 5.5 1.6 - - - +
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Residues in contact with LYS 299 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295B GLU* 3.2 25.7 + - - +
296B LEU* 3.1 24.3 + - + +
298B ILE* 1.3 77.6 - - + +
300B ILE* 1.3 57.1 + - - +
302B ASN 3.3 0.7 + - - -
303B GLY 2.9 9.2 + - - -
304B GLU* 2.8 65.4 + - + +
305B GLY 4.4 9.2 + - - +
306B VAL* 4.1 26.0 - - + -
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Residues in contact with ILE 300 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137B PRO* 3.4 30.9 - - + +
138B VAL 4.7 5.8 - - - +
139B VAL* 4.6 11.2 - - + -
150B ILE* 4.3 5.4 - - + -
296B LEU 3.1 14.5 + - - +
297B LEU* 3.6 8.7 - - + +
299B LYS* 1.3 72.9 - - - +
301B ILE* 1.3 67.7 + - - +
303B GLY* 3.1 13.2 + - - -
304B GLU 5.2 1.8 - - - +
306B VAL* 3.8 26.5 - - + -
308B ILE* 4.2 16.4 - - + -
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Residues in contact with ILE 301 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63B ILE* 4.7 2.2 - - + -
91B TYR* 3.7 23.1 - - + +
118B ALA* 3.5 40.4 - - + +
119B GLY* 4.4 0.9 - - - +
137B PRO* 3.8 15.8 - - + +
297B LEU* 2.8 31.5 + - + +
298B ILE* 3.6 28.5 - - + +
300B ILE* 1.3 78.8 - - - +
302B ASN* 1.3 66.1 + - - +
303B GLY 3.4 0.3 + - - -
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Residues in contact with ASN 302 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91B TYR* 4.8 3.3 + - - -
298B ILE* 2.9 42.2 + - - +
301B ILE* 1.3 82.3 - - - +
303B GLY* 1.3 61.8 + - - +
304B GLU* 3.2 34.5 + - + +
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Residues in contact with GLY 303 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299B LYS 2.9 5.0 + - - -
300B ILE* 3.1 11.5 + - - -
301B ILE 3.2 1.2 + - - -
302B ASN* 1.3 79.8 - - - +
304B GLU* 1.3 64.3 + - - +
305B GLY 4.1 0.3 + - - -
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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