Contacts of the helix formed by residues 293 - 308 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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291A GLY* 3.5 3.2 - - - -
292A THR* 1.3 79.4 + - - +
294A LYS* 1.3 67.2 + - - +
295A THR 3.3 2.9 - - - -
296A LEU* 3.1 18.3 + - - +
297A LEU* 3.0 23.9 + - - +
331A TRP* 6.3 1.1 - - - -
440A LEU* 3.7 6.7 - - - -
451A ARG* 4.9 2.5 - - - -
470A PHE* 5.2 3.7 - - - -
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Residues in contact with LYS 294 (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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286A ALA* 3.2 31.8 - - + +
287A THR 4.3 0.2 - - - -
288A GLY* 3.1 21.5 + - - +
289A ALA 2.8 23.6 + - - -
290A THR* 3.8 4.6 - - - +
291A GLY 4.3 3.2 - - - +
292A THR* 3.5 19.9 + - - +
293A GLY* 1.3 75.7 - - - +
295A THR* 1.3 58.5 + - - +
297A LEU* 3.1 9.7 + - - +
298A VAL* 2.9 31.8 + - - +
378A ASP* 5.2 0.9 - - - +
413A THR* 3.9 18.1 - - + +
414A ASN 4.2 1.3 - - - +
415A THR* 2.8 40.9 + - - +
440A LEU* 3.6 10.4 - - + +
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Residues in contact with THR 295 (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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293A GLY* 3.3 1.0 - - - -
294A LYS* 1.3 74.1 - - - +
296A LEU* 1.3 59.7 + - - +
298A VAL* 3.4 5.1 + - + +
299A SER* 2.8 40.1 + - - +
318A GLU* 5.7 0.5 + - - -
319A GLU* 3.5 26.0 + - - +
324A LEU* 4.5 9.9 - - + -
327A ASN* 6.4 0.7 - - + -
331A TRP* 4.5 14.1 - - + -
378A ASP* 2.7 31.8 + - - +
459B ARG* 6.0 0.2 + - - -
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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
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293A GLY* 3.1 19.1 + - - +
295A THR* 1.3 74.8 - - - +
297A LEU* 1.3 65.8 + - + +
299A SER* 3.1 13.1 + - - -
300A ARG* 3.1 20.0 + - - +
331A TRP* 3.5 59.6 - - + +
333A MET* 4.9 2.0 - - - -
470A PHE* 5.7 4.0 - - + -
472A ILE* 4.1 23.6 - - + -
476A GLY* 4.2 3.8 - - - -
477A PRO* 4.1 39.0 - - + -
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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
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265A SER 4.4 2.4 - - - +
267A VAL* 4.1 17.6 - - + +
270A LEU* 3.7 24.9 - - + -
286A ALA* 4.5 11.9 - - + -
293A GLY 3.0 13.5 + - - +
294A LYS* 3.1 8.3 + - - +
296A LEU* 1.3 77.2 - - + +
298A VAL* 1.3 61.2 + - - +
300A ARG* 3.8 4.8 + - - +
301A PHE* 3.2 23.6 + - - +
411A LEU* 3.9 10.0 - - + +
438A ILE* 3.7 31.9 - - + -
440A LEU* 4.0 24.5 - - + -
453A ILE* 4.3 3.8 - - + -
470A PHE* 6.3 3.4 - - + -
477A PRO* 5.4 7.6 - - + -
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Residues in contact with VAL 298 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286A ALA* 6.0 0.4 - - + -
294A LYS 2.9 15.7 + - - +
295A THR* 3.5 11.0 - - + +
296A LEU 3.2 0.2 - - - -
297A LEU* 1.3 72.2 - - - +
299A SER* 1.3 69.1 + - - +
301A PHE* 2.9 5.7 + - - +
302A VAL* 2.9 24.5 + - + +
314A LEU* 4.0 20.2 - - + -
376A ALA* 3.6 28.5 - - + -
377A ILE 5.2 0.4 - - - +
378A ASP* 4.3 7.0 - - + +
411A LEU* 3.7 19.7 - - + -
413A THR* 3.1 36.1 - - + -
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Residues in contact with SER 299 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295A THR* 2.8 27.4 + - - +
296A LEU* 3.1 9.2 + - - -
298A VAL* 1.3 77.4 - - - +
300A ARG* 1.3 56.2 - - - +
302A VAL* 3.5 4.4 + - - +
303A GLU* 3.0 27.0 + - - +
314A LEU* 5.9 0.6 - - - +
324A LEU 5.5 0.2 + - - -
328A ALA* 4.7 0.2 - - - +
331A TRP* 3.8 14.5 - - - -
333A MET* 3.6 22.6 - - - +
335A PHE* 3.7 32.0 - - - -
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Residues in contact with ARG 300 (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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265A SER 3.8 2.2 - - - +
266A GLY* 3.2 27.9 + - - +
267A VAL* 3.9 18.6 - - + +
268A VAL* 6.3 1.6 - - - +
296A LEU* 3.1 14.9 + - - +
297A LEU 4.2 3.6 - - - +
299A SER* 1.3 76.6 - - - +
301A PHE* 1.3 56.5 + - - +
303A GLU* 3.2 13.3 + - - +
304A ASN* 2.9 35.7 + - - +
331A TRP 4.3 4.8 + - - -
333A MET* 3.4 34.2 - - + +
475A LYS 3.7 23.3 + - - -
476A GLY* 4.6 1.6 - - - -
477A PRO* 3.8 26.8 + - - +
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Residues in contact with PHE 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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263A VAL* 5.9 1.1 - - + -
265A SER* 3.1 19.6 + - - +
278A PHE* 4.3 26.5 - + + -
284A ILE* 5.0 1.8 - - + -
297A LEU 3.2 15.3 + - - +
298A VAL 2.9 9.3 + - - +
300A ARG* 1.3 76.3 - - - +
302A VAL* 1.3 70.2 + - + +
304A ASN* 3.7 0.5 + - - +
305A ALA 3.6 3.1 + - - -
374A ARG* 3.5 71.4 + - + -
375A ILE 3.9 9.6 - - - -
376A ALA* 4.4 3.8 - - + -
409A THR* 3.8 26.5 - - + -
411A LEU* 3.7 39.7 - - + -
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Residues in contact with VAL 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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298A VAL* 2.9 19.1 + - + +
299A SER* 3.7 8.7 - - - +
301A PHE* 1.3 79.3 - - + +
303A GLU* 1.3 64.0 + - - +
305A ALA* 3.6 9.8 + - - +
306A CYS* 3.3 16.3 - - - -
312A ALA* 4.3 15.6 - - + +
313A ILE 4.8 4.9 - - - +
314A LEU* 4.7 10.3 - - + -
335A PHE* 4.4 10.1 - - + -
338A MET* 4.6 0.9 - - + -
344A LEU* 3.4 38.6 - - + -
374A ARG* 5.5 0.7 - - + +
375A ILE 5.9 0.2 - - - -
376A ALA* 3.8 27.4 - - + -
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Residues in contact with GLU 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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266A GLY* 5.2 2.1 - - - +
299A SER 3.0 14.7 + - - +
300A ARG* 3.2 22.1 + - - +
302A VAL* 1.3 73.2 - - - +
304A ASN* 1.3 59.0 + - - +
306A CYS* 2.8 25.5 + - - +
307A ALA* 2.8 21.5 + - + +
333A MET* 3.9 37.2 - - + +
338A MET* 3.3 31.6 - - + +
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Residues in contact with ASN 304 (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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264A SER* 3.0 44.3 + - - +
266A GLY* 3.8 15.1 - - - +
300A ARG 2.9 17.5 + - - +
301A PHE 3.7 7.0 - - - +
302A VAL 3.4 0.4 - - - -
303A GLU* 1.3 79.5 + - - +
305A ALA* 1.3 59.5 + - - +
307A ALA* 3.5 9.3 + - - +
308A ASN* 3.0 42.0 + - - +
374A ARG* 2.6 24.1 + - - +
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Residues in contact with ALA 305 (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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301A PHE 3.6 0.9 + - - +
302A VAL 3.6 11.6 + - - +
303A GLU 3.2 0.2 - - - -
304A ASN* 1.3 76.9 - - - +
306A CYS* 1.3 53.3 + - - +
308A ASN* 3.1 15.8 + - - +
310A GLU* 2.9 48.0 + - + +
312A ALA* 4.2 8.5 - - + -
374A ARG* 3.0 44.0 - - + +
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Residues in contact with CYS 306 (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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302A VAL* 3.3 18.2 - - - -
303A GLU 2.8 10.1 + - - +
305A ALA* 1.3 67.3 - - - +
307A ALA* 1.3 63.3 + - - +
308A ASN 3.2 1.6 - - - -
309A LYS* 3.3 8.8 + - - +
310A GLU 3.8 10.3 - - - -
312A ALA* 4.9 1.6 - - - -
338A MET* 3.8 23.1 - - + -
341A GLN* 5.7 0.5 + - - -
343A LEU* 3.6 37.8 - - + +
344A LEU* 3.8 30.1 - - - -
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Residues in contact with ALA 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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303A GLU* 2.8 19.3 + - + +
304A ASN* 3.5 17.5 - - - +
305A ALA 3.3 0.2 - - - -
306A CYS* 1.3 75.9 - - - +
308A ASN* 1.3 63.5 + - - +
309A LYS 3.4 1.9 + - - -
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Residues in contact with ASN 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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264A SER* 5.7 1.4 - - - -
304A ASN* 3.0 35.5 + - - +
305A ALA* 3.1 12.2 + - - +
307A ALA* 1.3 80.5 - - - +
309A LYS* 1.3 68.3 + - - +
310A GLU* 3.1 8.3 + - + +
374A ARG* 4.8 2.3 - - - +
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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