Contacts of the helix formed by residues 293 - 308 (chain B) in PDB entry 7V3X
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 GLY 293 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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291B GLY* 3.3 4.6 - - - -
292B THR* 1.3 79.6 - - - +
294B LYS* 1.3 65.6 + - - +
295B THR 3.5 1.8 - - - -
296B LEU* 3.3 12.6 - - - +
297B LEU* 3.1 27.1 + - - +
331B TRP* 6.3 0.4 - - - -
440B LEU* 3.7 7.9 - - - -
470B PHE* 5.0 1.3 - - - -
472B ILE* 4.2 16.6 - - - -
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Residues in contact with LYS 294 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286B ALA* 4.1 23.8 - - + +
287B THR 4.4 7.0 - - - +
288B GLY 3.4 15.8 + - - +
289B ALA 2.9 21.8 + - - +
290B THR* 3.8 5.9 - - - +
291B GLY 4.1 3.4 - - - +
292B THR* 3.4 23.8 - - - +
293B GLY* 1.3 75.9 - - - +
295B THR* 1.3 58.4 + - - +
297B LEU* 2.8 27.8 + - - +
298B VAL* 2.9 17.1 + - - +
318B GLU* 6.2 0.2 - - - -
378B ASP* 4.9 1.8 - - - +
379B SER* 6.1 0.9 - - - -
413B THR* 4.1 17.8 - - + +
414B ASN 3.8 9.0 - - - +
415B THR* 2.9 34.1 + - - +
440B LEU* 3.8 8.0 - - + +
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Residues in contact with THR 295 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293B GLY 3.5 0.2 - - - -
294B LYS* 1.3 77.3 - - - +
296B LEU* 1.3 56.5 + - - +
298B VAL* 3.5 8.1 - - + +
299B SER* 2.9 32.7 + - - +
318B GLU* 4.7 5.7 + - - -
319B GLU* 3.1 26.7 + - - +
324B LEU* 4.1 14.8 - - + -
327B ASN* 6.5 0.7 - - + -
331B TRP* 4.4 9.6 - - + -
378B ASP* 2.7 33.4 + - - +
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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
----------------------------------------------------------
293B GLY* 3.3 16.9 + - - +
294B LYS 3.1 0.4 - - - -
295B THR* 1.3 73.8 - - - +
297B LEU* 1.3 71.3 + - + +
299B SER* 2.9 15.7 + - - -
300B ARG* 3.0 31.4 + - + +
331B TRP* 3.6 49.6 - - + +
333B MET* 5.1 0.7 - - - -
470B PHE* 5.8 0.7 - - + -
472B ILE* 3.6 45.5 - - + -
476B GLY* 4.5 1.3 - - - -
477B PRO* 3.9 25.1 - - + -
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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
----------------------------------------------------------
265B SER 4.5 1.6 - - - +
270B LEU* 4.1 18.4 - - + -
278B PHE* 6.5 0.2 - - + -
286B ALA* 4.9 10.1 - - + -
293B GLY 3.1 20.3 + - - +
294B LYS* 2.8 12.5 + - - +
296B LEU* 1.3 80.6 - - + +
298B VAL* 1.3 53.8 - - - +
300B ARG* 3.3 7.7 + - + +
301B PHE* 2.8 36.6 + - - +
411B LEU* 3.9 9.8 - - + +
438B ILE* 4.0 29.4 - - + -
440B LEU* 4.2 17.5 - - + -
453B ILE* 4.4 7.6 - - + -
470B PHE* 6.1 2.7 - - + -
477B PRO* 4.8 15.9 - - + -
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Residues in contact with VAL 298 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294B LYS 2.9 9.3 + - - +
295B THR* 3.5 12.1 - - + +
297B LEU* 1.3 75.2 - - - +
299B SER* 1.3 61.5 + - - +
301B PHE* 3.5 2.6 - - - +
302B VAL* 3.1 24.6 + - - +
314B LEU* 3.2 36.3 - - + -
376B ALA* 4.0 11.2 - - + -
377B ILE 5.1 0.9 - - - +
378B ASP* 4.1 16.2 - - + +
411B LEU* 3.7 17.2 - - + +
413B THR* 3.0 37.9 - - + -
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Residues in contact with SER 299 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295B THR* 2.9 22.5 + - - +
296B LEU* 2.9 12.2 + - - -
298B VAL* 1.3 74.0 - - - +
300B ARG* 1.3 58.8 + - - -
302B VAL* 3.0 6.9 + - - +
303B GLU 2.9 25.1 + - - -
314B LEU* 5.9 0.5 - - - +
324B LEU* 5.7 2.6 - - - +
328B ALA* 4.6 2.4 - - - +
331B TRP* 4.1 13.6 - - - -
333B MET* 3.3 25.9 - - - +
335B PHE* 3.7 25.1 - - - -
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Residues in contact with ARG 300 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265B SER 3.7 4.3 - - - +
266B GLY* 2.9 42.5 + - - +
267B VAL* 4.1 13.3 - - + +
268B VAL 5.4 0.2 - - - +
296B LEU* 3.0 30.3 + - + +
297B LEU* 3.8 9.4 - - + +
299B SER* 1.3 70.9 - - - +
301B PHE* 1.3 60.8 - - - +
303B GLU* 3.8 21.3 + - - +
304B ASN* 3.1 26.9 + - - +
331B TRP* 5.3 1.4 + - - +
333B MET* 3.6 12.4 - - + -
475B LYS 2.7 29.3 + - - -
476B GLY* 3.8 0.8 - - - -
477B PRO* 3.5 30.3 + - + +
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Residues in contact with PHE 301 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263B VAL* 6.3 0.2 - - + -
265B SER 3.3 15.4 + - - +
278B PHE* 4.4 19.5 - + - -
284B ILE* 5.1 1.6 - - + -
297B LEU 2.8 21.9 + - - +
298B VAL 3.5 2.5 - - - +
299B SER 3.2 0.2 - - - -
300B ARG* 1.3 74.8 - - - +
302B VAL* 1.3 63.6 - - + +
305B ALA 3.6 3.3 + - - -
374B ARG* 3.0 69.8 + - + +
375B ILE 3.4 23.6 - - - -
376B ALA* 4.4 9.9 - - + -
409B THR* 3.6 39.0 - - + -
411B LEU* 3.3 35.2 - - + -
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Residues in contact with VAL 302 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298B VAL 3.1 16.4 + - - +
299B SER* 3.0 11.2 + - - +
301B PHE* 1.3 79.1 - - + +
303B GLU* 1.3 66.7 + - - +
305B ALA* 3.2 20.7 - - - +
306B CYS* 3.4 8.5 + - - -
312B ALA* 4.5 13.5 - - + +
313B ILE 4.8 1.3 - - - +
314B LEU* 4.5 16.6 - - + -
335B PHE* 4.8 10.5 - - + -
344B LEU* 3.3 38.4 - - + -
376B ALA* 4.1 21.5 - - + -
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Residues in contact with GLU 303 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299B SER 2.9 5.7 + - - +
300B ARG* 3.8 15.9 + - - +
302B VAL* 1.3 75.7 - - - +
304B ASN* 1.3 54.3 + - - +
306B CYS* 2.7 33.2 + - + +
307B ALA* 2.8 20.6 + - + +
332B GLY 5.1 1.8 - - - +
333B MET* 3.0 51.8 - - + +
335B PHE* 5.6 2.7 - - + -
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Residues in contact with ASN 304 (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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264B SER* 3.2 35.7 + - - -
266B GLY* 3.7 15.8 - - - -
300B ARG 3.1 15.1 + - - +
303B GLU* 1.3 80.6 - - - +
305B ALA* 1.3 61.3 + - - +
307B ALA* 3.3 12.6 - - - +
308B ASN* 3.0 33.1 + - - +
374B ARG* 3.2 25.8 + - - +
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Residues in contact with ALA 305 (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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301B PHE 3.6 2.8 + - - +
302B VAL 3.2 14.3 + - - +
303B GLU 3.1 0.2 - - - -
304B ASN* 1.3 78.2 + - - +
306B CYS* 1.3 56.9 + - - +
308B ASN* 3.1 10.5 + - - -
310B GLU* 2.9 45.6 + - + +
311B ARG 4.6 0.2 - - - +
312B ALA* 4.1 15.3 - - + -
374B ARG* 3.4 35.4 - - + +
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Residues in contact with CYS 306 (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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302B VAL* 3.6 14.1 - - - -
303B GLU* 2.7 18.3 + - + +
305B ALA* 1.3 73.1 - - - +
307B ALA* 1.3 61.2 + - - +
309B LYS* 3.2 13.2 + - - +
310B GLU 3.8 5.2 - - - -
312B ALA* 5.6 0.2 - - - -
338B MET* 3.6 30.3 - - + -
343B LEU* 3.2 48.5 - - + +
344B LEU* 3.7 8.7 - - - -
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Residues in contact with ALA 307 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303B GLU* 2.8 16.6 + - + +
304B ASN* 3.3 19.1 - - - +
305B ALA 3.2 0.2 - - - -
306B CYS* 1.3 75.9 - - - +
308B ASN* 1.3 63.3 + - - +
309B LYS* 3.3 18.1 + - - +
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Residues in contact with ASN 308 (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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304B ASN* 3.0 27.8 + - - +
305B ALA* 3.1 7.9 + - - +
307B ALA* 1.3 82.8 - - - +
309B LYS* 1.3 71.0 + - - +
310B GLU* 3.0 11.5 + - + +
374B ARG* 6.1 1.1 - - - +
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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