Contacts of the helix formed by residues 285 - 303 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154A SER* 3.6 14.4 - - - +
283A ASN* 3.8 15.3 - - - +
284A GLN* 1.3 78.4 - - - +
286A ILE* 1.3 65.7 + - - +
287A GLU 3.2 2.9 - - - -
288A ALA* 3.1 13.8 + - + +
289A LEU* 2.9 24.1 + - + +
313A MET* 3.5 24.0 - - + -
314A GLU 3.3 28.7 - - - +
315A VAL* 4.5 0.7 - - + -
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Residues in contact with ILE 286 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A PHE* 3.7 36.8 - - + -
77A GLN* 3.8 34.5 - - + +
78A MET* 3.8 21.8 - - + -
81A VAL* 3.9 29.4 - - + -
267A ASP 5.4 0.4 - - - +
268A ASN 5.1 8.1 - - - +
269A SER* 5.7 0.2 - - - -
284A GLN 2.9 14.3 + - - +
285A PRO* 1.3 70.7 - - - +
287A GLU* 1.3 60.2 + - + +
289A LEU* 3.7 7.9 - - - +
290A ALA* 2.8 28.9 + - - +
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Residues in contact with GLU 287 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A VAL* 3.5 29.1 - - + +
85A TYR* 2.5 41.0 + - - +
285A PRO 3.2 0.6 - - - -
286A ILE* 1.3 80.1 - - + +
288A ALA* 1.3 58.7 + - - +
291A TYR* 2.9 31.5 + - - +
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Residues in contact with ALA 288 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285A PRO* 3.1 21.8 + - + +
287A GLU* 1.3 75.8 - - - +
289A LEU* 1.3 64.9 + - - +
291A TYR* 3.8 6.7 - - - +
292A THR* 2.8 31.5 + - - +
313A MET* 4.0 21.1 - - + -
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Residues in contact with LEU 289 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A PHE* 4.4 2.5 - - + -
78A MET* 4.1 24.7 - - + -
141A PHE* 4.2 11.0 - - + -
152A ILE* 3.9 12.3 - - + -
153A SER 3.7 25.4 - - - +
154A SER* 3.5 19.1 - - - +
284A GLN* 4.0 14.4 - - + +
285A PRO* 2.9 27.4 + - + +
286A ILE* 3.7 4.3 - - - +
288A ALA* 1.3 76.2 - - - +
290A ALA* 1.3 59.3 + - - +
292A THR* 3.3 3.9 + - - -
293A ILE* 2.9 36.9 + - + +
313A MET* 3.7 23.1 - - + -
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Residues in contact with ALA 290 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A MET* 4.8 2.2 - - - +
81A VAL* 3.6 25.8 - - + -
82A ILE* 3.7 32.5 - - + +
85A TYR* 3.8 6.5 - - + -
286A ILE* 2.8 19.3 + - + +
287A GLU 3.9 0.2 - - - +
289A LEU* 1.3 73.9 - - - +
291A TYR* 1.3 65.6 + - - +
293A ILE* 3.4 2.8 + - - +
294A ILE* 3.1 29.5 + - - +
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Residues in contact with TYR 291 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85A TYR* 3.7 38.7 - + + +
287A GLU 2.9 19.0 + - - +
288A ALA* 3.8 6.1 - - - +
290A ALA* 1.3 77.9 - - - +
292A THR* 1.3 68.9 + - - +
294A ILE* 3.8 1.4 - - - +
295A GLU* 2.8 70.7 + - + +
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Residues in contact with THR 292 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152A ILE* 4.1 17.3 - - + -
288A ALA* 2.8 22.2 + - - +
289A LEU 3.7 3.1 - - - -
291A TYR* 1.3 86.8 - - - +
293A ILE* 1.3 66.4 + - - +
295A GLU* 3.7 3.5 - - - +
296A LEU* 2.9 51.0 + - + +
311A TYR* 3.7 20.4 - - + -
313A MET* 3.9 16.1 - - + +
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Residues in contact with ILE 293 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A MET* 4.2 22.2 - - + -
82A ILE* 4.2 13.2 - - + -
121A ILE* 3.7 43.3 - - + -
139A VAL* 3.9 8.4 - - + +
140A ALA 6.0 0.4 - - - -
141A PHE* 4.4 22.0 - - + -
152A ILE* 4.0 30.1 - - + -
289A LEU* 2.9 27.3 + - + +
290A ALA* 3.8 3.8 - - - +
292A THR* 1.3 76.1 - - - +
294A ILE* 1.3 60.6 + - + +
296A LEU* 3.9 0.5 - - - +
297A LEU* 2.9 28.2 + - - +
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Residues in contact with ILE 294 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A ILE* 4.3 13.9 - - + -
82A ILE* 3.9 27.1 - - + +
85A TYR* 3.7 35.2 - - + +
86A ALA* 4.0 20.6 - - + +
89A LYS* 3.8 22.4 - - + +
93A LEU* 5.4 0.2 - - + -
121A ILE* 4.0 14.4 - - + -
290A ALA 3.1 16.6 + - - +
291A TYR 3.9 2.5 - - - +
293A ILE* 1.3 76.1 - - + +
295A GLU* 1.3 66.2 + - - +
297A LEU* 3.3 3.5 + - + +
298A ILE* 2.9 28.4 + - + +
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Residues in contact with GLU 295 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89A LYS* 2.1 41.2 + - - +
291A TYR* 2.8 66.0 + - + +
292A THR* 3.7 6.3 - - - +
294A ILE* 1.3 73.7 - - - +
296A LEU* 1.3 66.1 - - + +
298A ILE* 3.5 3.1 + - - +
299A LYS* 3.2 38.5 + - - +
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Residues in contact with LEU 296 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139A VAL* 4.3 7.6 - - + -
150A ILE* 3.8 24.1 - - + +
152A ILE* 3.9 7.0 - - + -
292A THR* 2.9 36.1 + - + +
293A ILE* 4.0 2.5 - - - +
295A GLU* 1.3 77.5 - - + +
297A LEU* 1.3 66.1 + - - +
299A LYS* 3.1 20.4 + - - +
300A ILE* 3.1 25.0 + - - +
306A VAL* 4.0 17.7 - - + -
311A TYR* 3.6 51.6 - - + +
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Residues in contact with LEU 297 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A ILE* 3.7 44.2 - - + -
119A GLY* 4.3 1.6 - - - -
120A ILE 3.9 14.6 - - - +
121A ILE* 3.9 17.3 - - + -
137A PRO* 3.8 36.1 - - + +
138A VAL 4.1 0.2 - - - +
139A VAL* 3.9 21.0 - - + +
293A ILE 2.9 19.8 + - - +
294A ILE* 3.9 5.2 - - + +
296A LEU* 1.3 76.8 - - - +
298A ILE* 1.3 58.4 + - + +
300A ILE* 3.1 5.0 + - + +
301A ILE* 2.8 39.0 + - + +
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Residues in contact with ILE 298 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A ILE* 4.7 5.8 - - + -
89A LYS* 4.0 33.4 - - + +
91A TYR* 3.2 45.1 - - + +
294A ILE* 2.9 23.9 + - + +
295A GLU 3.8 4.5 - - - +
297A LEU* 1.3 76.1 - - + +
299A LYS* 1.3 64.9 + - + +
301A ILE* 3.7 12.7 - - + +
302A ASN* 2.9 44.4 + - - +
304A GLU* 5.4 1.1 - - - +
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Residues in contact with LYS 299 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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295A GLU* 3.2 28.6 + - - +
296A LEU* 3.1 24.3 + - + +
298A ILE* 1.3 77.4 - - + +
300A ILE* 1.3 56.9 + - - +
302A ASN 3.3 0.9 + - - -
303A GLY 2.9 8.8 + - - -
304A GLU* 2.8 59.4 + - + +
305A GLY 4.3 7.1 + - - +
306A VAL* 4.0 33.0 - - + -
311A TYR* 5.8 0.7 - - - -
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Residues in contact with ILE 300 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137A PRO* 3.5 30.5 - - + +
138A VAL 4.8 6.1 - - - +
139A VAL* 4.7 11.4 - - + -
150A ILE* 4.4 4.5 - - + -
296A LEU 3.1 16.5 + - - +
297A LEU* 3.6 8.7 - - + +
299A LYS* 1.3 76.1 - - - +
301A ILE* 1.3 64.5 + - - +
303A GLY* 3.1 13.1 + - - +
304A GLU 5.2 1.8 - - - +
306A VAL* 3.8 25.4 - - + -
308A ILE* 4.2 17.5 - - + -
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Residues in contact with ILE 301 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63A ILE* 4.7 2.2 - - + -
91A TYR* 3.7 23.8 - - + +
118A ALA* 3.5 39.3 - - + +
119A GLY 4.5 0.9 - - - +
137A PRO* 3.9 16.7 - - + +
297A LEU* 2.8 35.0 + - + +
298A ILE* 3.7 25.1 - - + +
300A ILE* 1.3 80.0 - - - +
302A ASN* 1.3 66.9 + - - +
303A GLY 3.5 0.5 + - - -
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Residues in contact with ASN 302 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91A TYR* 4.7 3.5 + - - -
298A ILE* 2.9 38.3 + - - +
299A LYS 3.9 0.2 - - - +
301A ILE* 1.3 87.5 - - - +
303A GLY* 1.3 60.7 + - - +
304A GLU* 3.2 32.5 + - - +
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Residues in contact with GLY 303 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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299A LYS 2.9 5.0 + - - -
300A ILE* 3.1 11.7 + - - -
301A ILE 3.3 1.2 + - - -
302A ASN* 1.3 79.1 - - - +
304A GLU* 1.3 64.0 + - - +
305A GLY 4.0 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
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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