Contacts of the helix formed by residues 389 - 401 (chain A) in PDB entry 4RYD
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 THR 389 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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282A ARG* 3.9 2.4 + - - -
284A GLY 5.6 0.4 - - - +
285A LEU* 3.3 33.9 - - + +
387A ASN 4.2 1.6 - - - +
388A LEU* 1.3 77.5 - - - +
390A TRP* 1.3 67.7 + - - +
391A ARG* 3.3 10.7 + - - +
392A ASP* 2.9 37.1 + - - +
393A MET* 3.1 21.7 + - - +
443A THR* 4.0 17.3 - - + -
444A VAL* 4.6 3.1 - - - +
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Residues in contact with TRP 390 (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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278A VAL* 3.4 45.6 + - + +
282A ARG* 3.9 0.8 - - - +
285A LEU 2.9 16.5 + - - -
286A GLY 3.9 4.0 - - - +
287A SER 3.8 22.2 - - - +
288A ILE* 3.6 15.8 - - + +
312A ILE* 3.4 28.7 - - + -
313A TYR* 4.1 20.2 - + - +
315A LEU* 5.6 1.6 - - - +
389A THR* 1.3 76.4 - - - +
391A ARG* 1.3 93.3 + - + +
393A MET* 3.6 4.2 + - - +
394A GLN* 3.5 35.6 + - - +
447A GLN* 3.8 15.3 - - - -
486A HIS* 4.4 5.8 - + - -
602A FMT 3.8 23.9 + - - -
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Residues in contact with ARG 391 (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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389A THR* 3.1 8.2 + - - +
390A TRP* 1.3 118.3 - - + +
392A ASP* 1.3 65.8 + - - +
393A MET 3.1 1.3 - - - -
394A GLN* 3.0 8.4 + - - +
395A HIS* 3.0 29.4 + - + -
444A VAL* 3.6 21.7 + - + +
445A ALA 2.9 31.1 + - - -
446A PRO* 3.8 1.4 - - - +
447A GLN* 3.3 36.3 - - - +
485A GLU* 2.8 42.1 + - - +
486A HIS* 5.4 3.1 - - + -
539A TRP* 4.7 1.5 - - + -
573A THR* 3.3 14.1 - - - +
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Residues in contact with ASP 392 (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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388A LEU* 3.6 15.2 - - + -
389A THR* 2.9 42.3 + - - +
391A ARG* 1.3 75.1 - - - +
393A MET* 1.3 63.8 + - - +
395A HIS* 3.0 8.5 + - - +
396A LEU* 2.9 26.8 + - - +
441A TRP* 2.9 31.7 + - - +
443A THR* 3.4 19.2 + - - -
444A VAL* 2.9 27.8 + - - +
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Residues in contact with MET 393 (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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288A ILE* 4.1 13.9 - - + -
315A LEU* 4.3 16.2 - - + -
378A ILE* 3.8 29.2 - - + +
381A THR* 3.9 11.9 - - + -
382A LEU* 3.7 36.8 - - + -
388A LEU* 3.7 19.3 - - + +
389A THR 3.1 8.2 + - - +
390A TRP 3.7 10.5 - - - +
391A ARG 3.1 0.2 - - - -
392A ASP* 1.3 80.2 - - - +
394A GLN* 1.3 61.7 + - - +
396A LEU* 3.4 7.2 + - - +
397A VAL* 3.2 23.0 + - + +
434A MET* 3.8 25.8 - - - -
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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
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312A ILE 2.9 23.4 + - - +
313A TYR 4.4 4.6 + - - -
314A THR 4.2 10.6 + - - +
315A LEU* 3.8 24.9 - - + +
337A LEU* 3.9 21.5 - - + +
390A TRP* 3.5 27.0 + - - +
391A ARG* 3.0 10.0 + - - +
393A MET* 1.3 74.0 - - - +
395A HIS* 1.3 65.0 + - - +
397A VAL* 3.3 3.4 + - - +
398A VAL* 3.0 27.2 + - - +
486A HIS* 2.6 30.5 + - - -
536A THR* 5.6 0.2 - - - +
539A TRP* 3.8 17.1 - - + -
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Residues in contact with HIS 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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391A ARG* 3.0 26.7 + - + -
392A ASP 3.0 8.4 + - - +
394A GLN* 1.3 77.8 - - - +
396A LEU* 1.3 63.1 + - - +
398A VAL* 3.2 3.7 + - - +
399A GLN* 2.9 30.9 + - - +
441A TRP* 3.6 25.4 - + + -
444A VAL* 3.7 25.3 - - + +
483A ARG* 4.6 14.3 + - - -
485A GLU* 2.9 34.1 + - + -
539A TRP* 3.2 36.3 + + - +
540A ASP* 4.2 15.5 + - - -
573A THR* 6.2 0.4 - - + -
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Residues in contact with LEU 396 (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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381A THR* 3.6 17.7 - - + -
388A LEU* 3.5 35.9 - - + -
392A ASP 2.9 17.4 + - - +
393A MET* 3.6 10.3 - - - +
394A GLN 3.3 0.2 - - - -
395A HIS* 1.3 77.0 - - - +
397A VAL* 1.3 57.0 + - - +
400A THR* 2.8 36.3 + - + +
434A MET* 3.7 15.0 - - + +
437A LEU* 3.6 39.3 - - + -
438A ALA* 3.9 8.1 - - + -
441A TRP* 3.7 25.1 - - + -
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Residues in contact with VAL 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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315A LEU* 4.0 18.8 - - + -
317A ILE* 5.8 2.0 - - + -
337A LEU* 4.0 20.9 - - + +
338A ALA* 3.5 31.4 - - + -
378A ILE* 5.2 4.0 - - + -
393A MET* 3.2 15.7 + - + +
394A GLN 3.6 6.7 - - - +
395A HIS 3.3 0.2 - - - -
396A LEU* 1.3 72.5 - - - +
398A VAL* 1.3 66.5 + - - +
400A THR* 4.1 0.4 - - - -
401A SER* 2.6 34.6 + - - +
429A LEU* 3.7 10.3 - - + -
434A MET* 3.8 24.5 - - + -
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Residues in contact with VAL 398 (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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337A LEU* 3.9 24.9 - - + -
394A GLN 3.0 17.0 + - - +
395A HIS 3.6 6.7 - - - +
397A VAL* 1.3 77.9 - - - +
399A GLN* 1.3 63.6 + - + +
400A THR 3.6 0.2 + - - -
401A SER 4.0 5.0 + - - +
418A ARG* 3.6 36.8 - - - +
426A TYR* 3.9 40.6 - - + +
539A TRP* 3.8 33.2 - - + +
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Residues in contact with GLN 399 (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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395A HIS* 2.9 19.3 + - - +
396A LEU 4.0 2.9 - - - +
397A VAL 3.3 0.2 - - - -
398A VAL* 1.3 80.7 - - + +
400A THR* 1.3 60.6 + - - +
401A SER 4.7 1.9 - - - +
418A ARG* 3.5 29.9 + - - +
437A LEU* 3.7 23.6 - - + +
441A TRP* 3.6 30.9 - - - -
483A ARG* 5.1 8.5 - - - +
540A ASP* 4.6 9.8 + - - +
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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
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396A LEU* 2.8 22.0 + - + +
397A VAL 4.0 0.5 + - - -
399A GLN* 1.3 78.1 - - - +
401A SER* 1.3 65.4 + - - +
402A LYS* 2.9 30.4 + - - +
429A LEU* 6.0 0.2 - - - +
430A ASP* 3.7 8.1 + - - +
433A ALA* 3.7 34.5 - - + +
434A MET* 3.1 24.1 - - - +
437A LEU* 3.6 26.9 - - + -
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Residues in contact with SER 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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338A ALA* 3.7 1.8 - - - +
397A VAL* 2.6 37.0 + - - +
398A VAL 4.0 4.4 + - - +
399A GLN 3.6 2.9 - - - +
400A THR* 1.3 78.8 + - - +
402A LYS* 1.3 63.2 + - - +
403A PRO* 3.6 5.2 - - - +
426A TYR* 3.4 29.5 - - - +
427A GLY 3.9 8.5 - - - -
428A LEU 3.3 10.5 - - - -
429A LEU* 3.6 15.8 - - - +
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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