Contacts of the helix formed by residues 295 - 313 (chain A) in PDB entry 3CVW
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 SER 295 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244A PHE* 3.4 10.3 - - - -
283A ILE* 6.5 0.4 - - - -
290A SER* 3.4 29.6 - - - -
291A GLN 3.5 6.7 + - - -
292A PRO* 3.1 19.1 - - - +
293A PRO 3.2 0.2 - - - -
294A VAL* 1.3 81.2 - - - +
296A LEU* 1.3 59.4 + - - +
297A ILE* 3.8 8.2 + - - +
298A GLY 2.9 17.7 + - - -
299A GLN* 2.9 31.7 + - - -
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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
----------------------------------------------------------
235A LEU* 5.5 1.1 - - + -
240A TRP* 4.0 22.2 - - + -
241A VAL* 4.2 15.8 + - + +
244A PHE* 3.5 43.5 + - + +
259A THR* 4.4 11.2 - - + -
275A PHE* 3.7 31.6 - - + -
279A LEU* 4.1 23.0 - - + +
290A SER* 4.7 0.2 + - - -
295A SER* 1.3 71.3 - - - +
297A ILE* 1.3 65.3 + - + +
299A GLN* 3.3 4.9 + - - +
300A LEU* 3.3 18.7 + - - +
521A FAD 4.0 16.8 - - - +
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Residues in contact with ILE 297 (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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276A ASN* 3.4 24.5 - - - +
279A LEU* 3.8 34.5 - - + +
280A LYS* 4.6 10.5 - - + +
283A ILE* 3.6 34.5 - - + -
292A PRO* 5.3 5.6 - - + -
295A SER* 3.3 7.6 - - - +
296A LEU* 1.3 73.3 - - + +
298A GLY* 1.3 59.8 + - - +
300A LEU* 3.1 5.8 + - + +
301A MET* 2.8 37.7 + - + +
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Residues in contact with GLY 298 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159A TYR* 2.9 27.5 + - - -
292A PRO* 4.1 9.1 - - - +
293A PRO 3.6 11.7 - - - -
295A SER* 2.9 24.1 + - - -
297A ILE* 1.3 76.9 - - - +
299A GLN* 1.3 55.7 + - - +
301A MET* 3.1 2.5 + - - -
302A TRP* 2.9 22.0 + - - -
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Residues in contact with GLN 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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244A PHE* 3.8 18.4 - - + -
246A LYS* 3.1 23.8 + - + +
293A PRO 2.8 27.5 + - - -
294A VAL 3.1 11.9 + - - -
295A SER 2.9 21.1 + - - +
296A LEU* 3.5 7.6 - - - +
298A GLY* 1.3 75.0 - - - +
300A LEU* 1.3 61.4 + - - +
302A TRP* 3.3 16.5 + - - +
303A ARG 3.4 2.9 + - - -
521A FAD 3.2 47.1 + - + +
8C 64T 2.8 35.4 + - - +
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Residues in contact with LEU 300 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141A ILE* 3.9 10.1 - - + -
265A LEU* 3.8 21.8 - - + -
272A ALA* 3.5 35.2 - - + +
275A PHE* 3.7 32.5 - - + -
276A ASN* 3.8 22.4 - - + +
279A LEU* 4.4 4.3 - - + -
296A LEU 3.3 8.8 + - - +
297A ILE* 3.1 11.3 + - + +
299A GLN* 1.3 79.5 - - - +
301A MET* 1.3 63.5 + - + +
303A ARG* 3.4 13.5 - - - +
304A GLU* 3.3 23.8 + - - +
521A FAD 3.7 7.6 + - - +
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Residues in contact with MET 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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141A ILE* 3.5 31.4 - - + -
142A TYR* 4.2 23.6 - - + -
159A TYR* 3.2 27.1 - - + +
162A PHE* 3.7 6.6 - - + -
163A LEU* 4.5 13.0 - - + -
166A VAL* 4.7 13.0 - - - -
276A ASN* 4.3 12.3 - - - +
292A PRO* 5.6 3.1 - - + -
297A ILE* 2.8 25.6 + - + +
298A GLY* 3.1 2.9 + - - +
300A LEU* 1.3 77.4 - - + +
302A TRP* 1.3 52.5 + - - +
304A GLU* 3.2 15.6 + - + +
305A PHE* 2.7 33.8 + - - +
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Residues in contact with TRP 302 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159A TYR* 3.4 36.3 - + + -
293A PRO* 3.4 26.2 + - + +
298A GLY 2.9 32.2 + - - -
299A GLN* 3.3 13.0 + - - +
301A MET* 1.3 74.1 - - - +
303A ARG* 1.3 58.6 + - - +
305A PHE* 3.1 19.4 + + - +
306A TYR* 3.0 55.4 + + - -
409A TRP* 3.7 24.9 - + - -
521A FAD 3.6 17.7 - + + +
8C 64T 3.2 72.0 - - + -
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Residues in contact with ARG 303 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139A HIS* 3.0 63.6 + - - -
140A THR* 4.0 3.4 - - - +
265A LEU* 3.4 29.4 + - - +
272A ALA* 3.4 21.5 - - - +
299A GLN 3.4 2.1 + - - +
300A LEU* 3.4 16.1 - - - +
302A TRP* 1.3 79.9 - - - +
304A GLU* 1.3 74.8 + - - +
306A TYR 3.6 0.2 + - - -
307A TYR* 3.1 40.9 + - + -
399A ASP* 5.1 2.4 + - - -
402A LEU* 3.8 23.0 - - + +
521A FAD 3.3 39.9 + - + +
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Residues in contact with GLU 304 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140A THR* 3.4 17.3 - - - -
141A ILE* 2.8 35.5 + - + +
142A TYR* 2.9 33.5 + - + +
162A PHE* 3.4 15.7 - - + -
300A LEU* 3.3 14.8 - - - +
301A MET* 3.2 27.0 + - + +
303A ARG* 1.3 89.1 + - - +
305A PHE* 1.3 60.3 + - - +
307A TYR* 3.6 5.9 + - - +
308A THR* 2.9 29.3 + - - -
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Residues in contact with PHE 305 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156A PRO 3.3 22.7 - - - -
157A ILE 4.2 7.0 - - - -
158A THR* 3.6 18.8 - - - -
159A TYR* 4.3 9.2 - + + -
162A PHE* 3.7 34.5 - + + -
301A MET 2.7 16.0 + - - +
302A TRP* 3.1 39.4 + + - +
304A GLU* 1.3 75.0 - - - +
306A TYR* 1.3 79.2 + + - +
308A THR* 3.3 11.8 + - - -
309A VAL* 3.4 16.3 + - + +
409A TRP* 5.3 0.2 - + - -
415A PHE* 3.7 39.3 - + + -
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Residues in contact with TYR 306 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302A TRP* 3.0 45.6 + + - +
305A PHE* 1.3 85.9 - + - +
307A TYR* 1.3 61.6 + - - +
309A VAL* 3.4 5.8 - - + +
310A ALA* 3.3 26.0 + - - +
316A PHE* 4.3 4.3 - + - -
401A ALA* 3.9 15.7 - - - +
402A LEU* 4.2 13.0 - - + -
405A GLY* 3.5 33.4 - - - -
406A ASN* 3.2 28.7 + - - -
409A TRP* 3.2 32.4 - - - +
415A PHE* 3.9 19.7 - + - -
521A FAD 3.5 18.6 - + - -
8C 64T 4.5 1.8 - - + +
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Residues in contact with TYR 307 (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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14A LYS* 2.8 25.6 + - - -
110A ASP* 4.3 3.1 - - - -
111A ILE* 3.3 56.8 - - + +
112A GLU* 5.3 1.8 - - + -
139A HIS* 2.8 27.9 + + - -
140A THR* 3.7 25.4 - - + -
144A PRO* 4.1 9.7 - - + +
303A ARG* 3.1 37.7 + - + +
304A GLU 3.9 5.2 - - - +
305A PHE 3.3 0.2 - - - -
306A TYR* 1.3 78.5 - - - +
308A THR* 1.3 59.2 + - - +
311A ALA* 3.3 8.7 + - - +
399A ASP* 2.7 39.4 + - - -
401A ALA* 4.3 4.3 - - + -
402A LEU* 3.6 12.1 - - + -
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Residues in contact with THR 308 (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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142A TYR 5.6 1.2 + - - -
144A PRO* 3.9 29.8 - - - +
147A VAL* 3.8 26.9 - - + +
148A ILE* 3.8 19.4 - - + +
155A ALA* 4.1 8.8 - - + +
156A PRO* 4.3 3.6 - - + -
162A PHE* 3.2 17.0 - - + -
304A GLU 2.9 16.1 + - - -
305A PHE* 3.7 7.2 - - - -
306A TYR 3.3 0.4 - - - -
307A TYR* 1.3 75.0 - - - +
309A VAL* 1.3 66.0 + - - +
311A ALA* 3.1 17.7 + - - +
312A ALA 3.8 0.3 + - - -
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Residues in contact with VAL 309 (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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155A ALA* 4.0 11.9 - - + -
156A PRO 3.3 28.0 - - - +
157A ILE* 4.6 0.2 - - - -
305A PHE* 3.4 16.6 + - + +
306A TYR* 3.4 19.3 - - + +
308A THR* 1.3 79.6 - - - +
310A ALA* 1.3 62.9 + - - +
312A ALA 3.7 1.2 + - - -
313A GLU 3.6 6.6 + - - -
316A PHE* 3.8 17.0 - - + -
324A TYR* 2.7 43.4 + - + +
415A PHE* 3.8 27.6 - - + -
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Residues in contact with ALA 310 (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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111A ILE* 3.8 10.4 - - + +
306A TYR 3.3 18.7 + - - +
308A THR 3.2 1.0 - - - -
309A VAL* 1.3 76.0 - - - +
311A ALA* 1.3 63.8 + - - +
312A ALA 3.2 1.1 - - - -
313A GLU 2.9 21.3 - - - +
314A PRO* 5.0 0.2 - - - +
316A PHE* 3.6 34.3 - - + -
400A TRP* 3.7 23.9 - - + -
401A ALA* 3.8 4.5 - - + -
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Residues in contact with ALA 311 (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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111A ILE* 3.7 24.9 - - + +
144A PRO* 3.7 20.2 - - + -
145A GLU* 5.4 4.5 - - + +
148A ILE* 4.3 8.3 - - + -
307A TYR 3.3 13.8 + - - +
308A THR 3.1 13.6 + - - +
310A ALA* 1.3 77.6 - - - +
312A ALA* 1.3 60.9 + - - +
313A GLU 5.1 0.3 - - - -
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Residues in contact with ALA 312 (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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148A ILE* 4.3 18.5 - - + +
154A LYS* 6.5 0.2 - - - -
155A ALA* 4.9 5.2 - - + +
308A THR 3.8 2.1 + - - +
309A VAL 3.7 1.5 + - - +
310A ALA 3.2 0.4 - - - -
311A ALA* 1.3 81.4 - - - +
313A GLU* 1.3 58.9 + - + +
314A PRO* 3.3 13.3 - - - +
324A TYR* 3.9 16.6 - - - +
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Residues in contact with GLU 313 (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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309A VAL 3.6 2.7 + - - +
310A ALA 2.9 19.9 + - - +
311A ALA 5.1 0.2 - - - -
312A ALA* 1.3 77.1 - - + +
314A PRO* 1.3 72.9 - - - +
315A ASN* 3.2 22.7 + - - +
316A PHE* 3.4 20.6 - - + +
321A GLY 2.8 23.6 - - - +
322A ASN* 3.4 17.7 - - - +
323A VAL* 2.8 36.5 + - + +
324A TYR* 3.6 22.2 - - + -
400A TRP* 3.9 1.2 - - - -
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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