Contacts of the helix formed by residues 388 - 406 (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 SER 388 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212A GLU* 5.5 0.5 + - - -
387A VAL* 1.3 77.5 - - - +
389A ASN* 1.3 53.8 + - - +
390A ASN* 4.0 7.8 + - - +
391A ALA* 3.1 23.4 + - - +
392A PHE* 2.7 31.2 + - - +
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Residues in contact with ASN 389 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387A VAL 3.9 1.8 + - - -
388A SER* 1.3 68.6 - - - +
390A ASN* 1.3 60.5 + - - +
392A PHE* 3.9 21.9 - - - -
393A ARG* 2.6 40.3 + - - +
427A ASP 4.7 1.1 - - - +
428A SER* 2.9 36.1 + - - +
429A HIS* 4.1 12.8 - - - +
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Residues in contact with ASN 390 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388A SER* 3.2 7.6 - - - +
389A ASN* 1.3 79.8 - - - +
391A ALA* 1.3 53.3 + - - +
393A ARG* 3.7 4.8 - - - +
394A GLN* 2.8 35.6 + - - +
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Residues in contact with ALA 391 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212A GLU* 4.6 13.7 - - - +
217A ARG* 5.3 14.7 + - - +
356A LEU* 3.4 13.9 - - + +
387A VAL* 3.6 13.5 - - + -
388A SER* 3.1 20.5 + - - +
390A ASN* 1.3 77.0 - - - +
392A PHE* 1.3 62.4 + - - +
394A GLN* 3.5 12.2 - - - +
395A PHE* 3.3 15.6 + - - +
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Residues in contact with PHE 392 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356A LEU* 3.6 8.7 - - + -
380A LEU* 3.4 38.1 - - + -
383A LEU* 4.0 8.1 - - + -
384A ALA* 3.5 31.9 - - + +
387A VAL* 3.7 7.5 - - + +
388A SER 2.7 19.3 + - - +
389A ASN* 3.6 13.0 - - - +
391A ALA* 1.3 71.1 - - - +
393A ARG* 1.3 62.5 + - - +
395A PHE* 2.9 39.7 + + - +
396A VAL* 3.1 31.9 + - + +
428A SER* 3.5 33.7 - - - -
430A ILE* 4.0 7.9 - - + -
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Residues in contact with ARG 393 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
389A ASN* 2.6 32.0 + - - +
390A ASN* 3.8 5.2 - - - +
392A PHE* 1.3 77.5 - - - +
394A GLN* 1.3 55.7 + - - +
396A VAL* 3.2 8.8 + - - +
397A ILE* 3.0 39.4 + - + +
428A SER 5.4 0.4 - - - +
429A HIS 6.1 0.2 - - - +
430A ILE* 4.7 10.5 - - + -
433A ILE* 5.9 3.5 - - + +
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Residues in contact with GLN 394 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217A ARG* 2.7 34.1 + - - +
234A GLU 5.9 0.4 + - - -
236A PRO* 3.6 17.0 - - - +
249A LEU* 4.2 29.1 - - + +
360A LEU* 5.6 1.3 - - - +
390A ASN 2.8 17.9 + - - +
391A ALA* 3.5 9.5 - - - +
392A PHE 3.2 0.2 - - - -
393A ARG* 1.3 74.8 - - - +
395A PHE* 1.3 62.4 + - - +
397A ILE* 3.4 10.3 + - - +
398A GLY* 3.1 19.6 + - - -
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Residues in contact with PHE 395 (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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356A LEU* 3.5 43.3 - - + -
359A HIS* 4.1 8.1 - - + -
360A LEU* 3.7 35.5 - - + +
363A ILE* 4.1 11.2 - - + -
377A ILE* 5.1 1.3 - - + -
380A LEU* 4.3 13.2 - - + -
383A LEU* 3.7 33.2 - - + -
391A ALA 3.3 4.8 + - - +
392A PHE* 2.9 26.4 + + - +
394A GLN* 1.3 79.4 - - - +
396A VAL* 1.3 60.0 + - + +
398A GLY* 3.3 3.1 + - - -
399A VAL* 3.0 56.7 + - + +
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Residues in contact with VAL 396 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
380A LEU* 4.4 17.7 - - + -
392A PHE* 3.1 47.8 + - + +
393A ARG* 3.2 9.2 + - - +
395A PHE* 1.3 77.6 - - + +
397A ILE* 1.3 68.4 + - + +
399A VAL* 3.0 6.0 + - - +
400A THR* 2.9 31.9 + - - +
430A ILE* 4.4 19.1 - - + +
433A ILE* 3.8 26.7 - - + -
434A THR* 6.5 0.4 - - + -
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Residues in contact with ILE 397 (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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249A LEU 5.4 8.1 - - - +
252A MET* 6.5 1.6 - - + -
393A ARG* 3.0 26.9 + - + +
394A GLN* 3.4 9.4 + - - +
396A VAL* 1.3 74.2 - - - +
398A GLY* 1.3 54.0 + - - +
400A THR* 3.6 5.5 - - - +
401A GLY* 2.9 33.1 + - - -
433A ILE* 3.7 32.5 - - + -
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Residues in contact with GLY 398 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252A MET* 6.3 2.5 - - - -
360A LEU* 4.3 19.4 - - - +
394A GLN 3.1 10.0 + - - -
395A PHE 3.6 4.3 - - - -
396A VAL 3.1 0.8 - - - -
397A ILE* 1.3 77.0 - - - +
399A VAL* 1.3 63.4 + - - +
401A GLY* 4.0 0.7 - - - -
402A TYR* 3.2 24.9 + - - +
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Residues in contact with VAL 399 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360A LEU* 4.2 11.7 - - + -
363A ILE* 4.3 18.4 - - + -
377A ILE* 3.7 27.1 - - + -
380A LEU* 5.7 1.3 - - + -
395A PHE* 3.0 55.4 + - + +
396A VAL* 3.9 4.7 - - - +
398A GLY* 1.3 70.4 - - - +
400A THR* 1.3 69.3 + - - +
402A TYR* 3.3 6.0 + - - +
403A ALA* 3.1 21.4 + - + +
412A PHE* 4.3 11.0 - - + -
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Residues in contact with THR 400 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283A ILE* 3.7 38.3 - - + +
396A VAL* 2.9 21.8 + - - +
397A ILE* 3.6 3.8 - - - +
399A VAL* 1.3 75.3 - - - +
401A GLY* 1.3 55.7 + - - +
403A ALA* 3.0 7.3 + - - +
404A LYS* 2.7 38.9 + - + +
412A PHE* 4.9 6.0 - - - -
433A ILE* 3.4 32.6 - - + +
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Residues in contact with GLY 401 (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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252A MET* 6.4 2.5 - - - -
253A ARG 6.4 0.2 - - - -
256A GLN* 2.9 33.0 - - - +
397A ILE* 2.9 21.4 + - - -
398A GLY* 4.1 1.3 - - - -
400A THR* 1.3 74.7 - - - +
402A TYR* 1.3 56.2 + - - +
404A LYS* 4.2 2.9 - - - -
405A GLN* 3.0 20.9 + - - +
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Residues in contact with TYR 402 (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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360A LEU* 5.8 3.4 - - + -
364A LYS* 4.2 22.2 - - + -
367A ILE* 3.7 45.4 - - + +
368A ASN* 2.8 35.3 + - - -
398A GLY 3.2 18.6 + - - +
399A VAL* 3.7 4.9 - - - +
400A THR 3.2 0.2 - - - -
401A GLY* 1.3 73.8 - - - +
403A ALA* 1.3 59.9 + - - +
405A GLN* 3.5 20.1 + - + +
406A GLU* 2.9 43.0 + - + +
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Residues in contact with ALA 403 (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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283A ILE* 4.6 11.2 - - + -
367A ILE* 5.6 6.1 - - + -
375A ILE* 5.8 4.7 - - + -
399A VAL* 3.1 13.8 + - + +
400A THR 3.0 8.4 + - - +
402A TYR* 1.3 78.7 - - + +
404A LYS* 1.3 57.4 + - - +
406A GLU* 4.9 0.4 - - - -
407A GLU* 3.0 7.8 + - - -
408A ILE* 2.6 57.1 + - + +
410A GLY* 5.1 4.0 - - - +
412A PHE* 5.2 6.3 - - + -
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Residues in contact with LYS 404 (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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256A GLN* 3.3 22.0 - - + +
257A ARG 3.9 16.8 - - - +
281A ASP* 4.8 11.9 - - - +
282A SER* 5.9 1.8 - - - +
283A ILE* 5.1 7.5 - - + +
400A THR* 2.7 26.9 + - + +
401A GLY* 3.9 2.9 - - - +
403A ALA* 1.3 73.0 - - - +
405A GLN* 1.3 58.9 + - - +
407A GLU* 3.4 13.7 + - - +
408A ILE 4.8 1.1 - - - -
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Residues in contact with GLN 405 (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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252A MET* 5.7 8.3 - - - +
253A ARG 4.6 2.0 - - - +
254A LEU* 3.3 30.3 + - + +
256A GLN* 3.2 29.9 + - + +
257A ARG* 5.2 1.7 + - - +
401A GLY 3.0 23.4 + - - +
402A TYR* 3.6 27.1 - - + +
404A LYS* 1.3 74.6 - - - +
406A GLU* 1.3 63.2 + - + +
407A GLU* 3.3 7.9 + - - +
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Residues in contact with GLU 406 (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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367A ILE* 5.5 5.2 - - + -
402A TYR* 2.9 35.9 + - + +
403A ALA* 4.4 2.2 - - - +
405A GLN* 1.3 77.0 - - + +
407A GLU* 1.3 70.7 + - - +
408A ILE* 3.2 6.9 + - + +
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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