Contacts of the helix formed by residues 355 - 371 (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 355 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215A ARG* 4.1 17.9 - - - +
216A ARG 5.0 8.0 + - - -
354A ALA* 1.3 72.6 - - - +
356A LEU* 1.3 58.1 + - - -
357A GLU* 3.5 2.7 - - - -
358A ASP* 3.8 11.9 + - - +
359A HIS* 2.9 36.8 + - - -
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Residues in contact with LEU 356 (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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217A ARG* 5.0 8.9 - - - +
351A PRO* 6.0 0.7 - - + +
354A ALA 5.8 0.2 - - - +
355A GLY* 1.3 73.2 - - - -
357A GLU* 1.3 60.8 + - - +
358A ASP 3.2 0.2 - - - -
359A HIS* 3.3 15.5 + - + +
360A LEU* 2.9 25.6 + - - +
383A LEU* 3.5 27.6 - - + +
387A VAL* 3.2 41.7 - - + -
391A ALA* 3.4 23.6 - - + +
392A PHE* 3.6 11.0 - - + -
395A PHE* 3.5 32.6 - - + -
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Residues in contact with GLU 357 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217A ARG* 4.4 14.6 - - + +
218A ARG 5.5 2.5 - - - +
236A PRO* 4.0 28.7 - - + -
237A PHE 4.5 13.5 - - - +
238A THR* 4.4 5.6 + - + +
247A PHE* 4.7 5.6 - - + -
356A LEU* 1.3 77.6 - - - +
358A ASP* 1.3 66.3 + - - +
360A LEU* 3.3 12.7 - - - +
361A GLN* 3.2 20.4 + - - +
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Residues in contact with ASP 358 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216A ARG 5.0 6.6 - - - +
237A PHE 5.5 0.3 - - - +
238A THR* 3.4 25.9 - - - +
354A ALA* 3.8 24.2 - - + -
355A GLY* 3.8 10.5 + - - +
356A LEU 3.2 0.4 - - - -
357A GLU* 1.3 77.8 - - - +
359A HIS* 1.3 59.4 + - - +
361A GLN* 3.2 5.9 + - - +
362A ILE* 3.0 34.8 + - + +
232B LYS* 4.9 15.2 - - - +
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Residues in contact with HIS 359 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317A TYR* 4.1 22.1 + + - +
349A ALA* 4.9 6.0 - - + +
350A TYR 3.6 18.6 - - - -
351A PRO* 3.1 28.2 + - + +
353A SER* 4.0 2.5 - - - -
354A ALA* 3.5 20.5 + - + +
355A GLY 2.9 23.3 + - - -
356A LEU* 3.5 14.6 - - + +
358A ASP* 1.3 72.9 - - - +
360A LEU* 1.3 66.0 + - - +
362A ILE* 3.2 13.4 + - - +
363A ILE* 3.0 27.6 + - - +
383A LEU* 3.8 17.5 - - + -
395A PHE* 4.1 15.0 - - + -
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Residues in contact with LEU 360 (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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236A PRO* 6.4 1.1 - - + -
247A PHE* 3.2 36.1 - - + -
356A LEU 2.9 12.9 + - - +
357A GLU* 3.3 15.7 - - - +
358A ASP 3.3 0.2 - - - -
359A HIS* 1.3 74.7 - - - +
361A GLN* 1.3 52.2 + - - +
363A ILE* 3.4 4.9 + - + +
364A LYS* 2.9 36.0 + - + +
394A GLN 5.6 0.7 - - - +
395A PHE* 3.7 27.7 - - + +
398A GLY* 4.3 16.8 - - - +
399A VAL* 4.2 26.5 - - + +
402A TYR* 5.8 3.4 - - + -
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Residues in contact with GLN 361 (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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238A THR* 4.2 20.0 - - + +
240A THR* 5.2 8.3 - - + -
245A ASN* 6.0 1.8 - - - -
247A PHE* 4.0 15.0 - - + -
357A GLU 3.2 10.0 + - - +
358A ASP* 3.2 12.1 + - - +
360A LEU* 1.3 74.1 - - - +
362A ILE* 1.3 59.6 + - + +
364A LYS* 2.9 4.6 + - - +
365A SER* 2.7 37.5 + - - -
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Residues in contact with ILE 362 (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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315A PHE* 5.8 1.1 - - + -
317A TYR* 5.9 2.7 - - - +
347A VAL* 4.9 16.4 - - + -
358A ASP* 3.0 27.1 + - + +
359A HIS* 3.5 14.8 - - - +
361A GLN* 1.3 75.3 - - + +
363A ILE* 1.3 59.2 + - + +
365A SER* 3.5 6.5 - - - -
366A GLU* 2.9 41.4 + - + +
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Residues in contact with ILE 363 (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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315A PHE* 3.1 39.7 - - + -
317A TYR* 3.6 20.9 - - + +
359A HIS 3.0 14.8 + - - +
360A LEU* 3.7 7.6 - - + +
362A ILE* 1.3 75.1 - - + +
364A LYS* 1.3 65.6 + - - +
366A GLU* 3.1 1.9 + - - +
367A ILE* 3.0 46.7 + - + +
375A ILE* 5.8 2.9 - - + -
377A ILE* 3.8 21.8 - - + -
395A PHE* 4.1 18.8 - - + -
399A VAL* 4.3 17.3 - - + -
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Residues in contact with LYS 364 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247A PHE* 4.9 12.6 - - + -
360A LEU* 2.9 25.9 + - + +
361A GLN* 3.6 7.2 - - - +
363A ILE* 1.3 73.2 - - - +
365A SER* 1.3 60.3 - - - +
367A ILE* 3.9 2.5 + - - +
368A ASN* 2.9 31.0 + - - +
402A TYR* 3.8 31.0 + - + -
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Residues in contact with SER 365 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361A GLN* 2.7 21.5 + - - -
362A ILE* 3.5 7.7 + - - -
364A LYS* 1.3 69.6 - - - +
366A GLU* 1.3 64.9 + - - +
368A ASN* 3.0 27.0 + - - +
369A ASP* 3.2 24.1 + - - +
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Residues in contact with GLU 366 (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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313A ILE* 3.3 25.0 - - + +
315A PHE* 4.1 8.5 - - + -
345A LYS* 2.8 38.7 + - - +
347A VAL* 4.2 20.4 - - + +
362A ILE* 2.9 34.4 + - + +
363A ILE 3.1 3.6 + - - +
365A SER* 1.3 75.7 + - - +
367A ILE* 1.3 64.5 + - - +
369A ASP* 3.2 17.7 + - - +
370A PHE* 3.3 10.7 + - - +
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Residues in contact with ILE 367 (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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313A ILE* 4.0 3.8 - - + -
315A PHE* 4.5 8.1 - - + -
363A ILE* 3.0 40.6 + - + +
364A LYS 3.9 4.5 - - - +
366A GLU* 1.3 75.7 - - - +
368A ASN* 1.3 54.4 + - - +
371A LYS* 2.6 39.7 + - - -
372A PRO* 3.2 23.6 - - + +
375A ILE* 5.2 11.0 - - + -
399A VAL* 6.0 2.5 - - + +
402A TYR* 3.7 37.2 - - + +
403A ALA* 5.6 8.1 - - + +
406A GLU* 5.5 6.1 - - + -
408A ILE* 5.3 8.5 - - + -
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Residues in contact with ASN 368 (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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364A LYS* 2.9 19.6 + - - +
365A SER* 3.0 10.9 + - - +
367A ILE* 1.3 78.0 - - - +
369A ASP* 1.3 62.4 + - - +
370A PHE 3.6 0.5 + - - -
371A LYS* 4.3 7.0 + - - +
402A TYR* 2.8 24.4 + - - -
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Residues in contact with ASP 369 (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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345A LYS* 5.0 9.6 - - - +
365A SER* 3.2 23.2 + - - +
366A GLU* 3.2 14.5 + - - +
368A ASN* 1.3 78.7 - - - +
370A PHE* 1.3 62.5 + - - +
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Residues in contact with PHE 370 (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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311A ARG* 3.9 23.4 - - + +
312A ALA 4.3 2.5 - - - -
313A ILE* 3.9 25.8 - - + -
342A ASN* 3.7 39.3 - - + -
343A LEU 3.3 24.9 - - - -
344A LEU 4.5 1.6 - - - -
345A LYS* 3.7 38.4 - - + +
366A GLU 3.3 12.8 + - - +
369A ASP* 1.3 83.9 - - + +
371A LYS* 1.3 70.1 + - - +
372A PRO* 3.4 1.7 - - + -
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Residues in contact with LYS 371 (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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311A ARG* 4.7 2.8 - - - +
367A ILE* 2.6 22.4 + - - +
368A ASN* 4.8 6.5 - - - +
370A PHE* 1.3 75.6 - - - +
372A PRO* 1.4 69.1 - - - +
373A ALA 3.8 0.7 + - - -
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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
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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