Contacts of the helix formed by residues 389 - 401 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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282F ARG* 4.1 3.2 + - - -
284F GLY 5.7 0.4 - - - +
285F LEU* 3.3 34.5 - - + +
387F ASN 4.3 0.9 - - - +
388F LEU* 1.3 76.5 - - - +
390F TRP* 1.3 69.2 + - - +
391F ARG* 3.3 10.5 + - - +
392F ASP* 2.9 34.0 + - - +
393F MET* 3.1 21.5 + - - +
443F THR* 3.8 18.8 - - + -
444F VAL* 4.6 3.2 - - + +
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Residues in contact with TRP 390 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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278F VAL* 3.3 44.2 + - + +
282F ARG* 4.1 0.6 - - - +
284F GLY 5.7 0.2 - - - -
285F LEU 2.9 18.5 + - - +
286F GLY 4.0 2.2 - - - +
287F SER 3.8 22.4 - - - +
288F ILE* 3.6 14.8 - - + +
312F ILE* 3.5 27.1 - - + -
313F TYR* 4.2 16.6 - + - +
315F LEU* 5.6 1.4 - - - +
389F THR* 1.3 77.0 - - - +
391F ARG* 1.3 93.2 + - + +
393F MET* 3.7 4.0 + - - +
394F GLN* 3.6 36.8 + - - +
447F GLN* 3.8 14.4 - - - -
486F HIS* 4.5 5.8 - + - -
601F FMT 3.7 29.5 + - - -
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Residues in contact with ARG 391 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
389F THR* 3.1 8.2 + - - +
390F TRP* 1.3 118.5 - - + +
392F ASP* 1.3 66.5 + - - +
393F MET 3.1 1.6 - - - -
394F GLN* 3.1 8.5 + - - +
395F HIS* 3.0 28.3 + - + -
444F VAL* 3.4 22.5 + - + +
445F ALA 2.9 29.5 + - - -
446F PRO* 4.0 1.6 - - - +
447F GLN* 3.4 35.5 - - - +
485F GLU* 2.9 42.4 + - - +
486F HIS* 5.3 4.3 - - + -
539F TRP* 4.7 1.5 - - + -
572F GLY 4.6 0.2 + - - -
573F THR* 3.3 14.5 - - - +
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Residues in contact with ASP 392 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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388F LEU* 3.5 18.2 - - + +
389F THR* 2.9 38.4 + - - +
391F ARG* 1.3 74.1 - - - +
393F MET* 1.3 63.5 + - - +
395F HIS* 3.0 9.6 + - - +
396F LEU* 2.9 26.5 + - - +
441F TRP* 2.8 33.5 + - - +
443F THR* 3.5 19.6 + - - +
444F VAL* 3.0 25.2 + - - +
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Residues in contact with MET 393 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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288F ILE* 4.3 14.4 - - + -
315F LEU* 4.4 15.3 - - + -
378F ILE* 3.7 33.9 - - + +
381F THR* 3.8 21.5 - - + -
382F LEU* 3.7 32.8 - - + -
388F LEU* 3.7 18.8 - - + -
389F THR 3.1 7.9 + - - +
390F TRP 3.7 10.1 - - - +
391F ARG 3.1 0.2 - - - -
392F ASP* 1.3 80.1 - - - +
394F GLN* 1.3 61.1 + - - +
396F LEU* 3.3 8.0 + - - +
397F VAL* 3.1 27.1 + - + +
434F MET* 3.9 16.4 - - - -
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Residues in contact with GLN 394 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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312F ILE 2.9 22.8 + - - -
313F TYR 4.3 2.8 + - - -
314F THR 4.0 13.6 + - - +
315F LEU* 3.9 25.4 - - + +
337F LEU* 4.0 21.6 - - + +
390F TRP* 3.6 25.7 + - - +
391F ARG* 3.1 9.6 + - - +
393F MET* 1.3 73.8 - - - +
395F HIS* 1.3 66.1 + - - +
397F VAL* 3.3 3.3 + - - +
398F VAL* 3.0 27.0 + - - +
486F HIS* 2.7 30.0 + - - -
539F TRP* 3.8 17.3 - - + -
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Residues in contact with HIS 395 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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391F ARG 3.0 25.4 + - - -
392F ASP 3.0 7.7 + - - +
394F GLN* 1.3 76.8 - - - +
396F LEU* 1.3 64.0 + - - +
398F VAL* 3.2 2.3 + - - +
399F GLN* 2.9 32.2 + - - +
441F TRP* 3.5 22.7 - + + -
444F VAL* 3.4 25.8 - - + +
483F ARG* 4.0 24.9 + - - -
485F GLU* 2.8 34.5 + - + -
539F TRP* 3.0 39.0 + + - +
540F ASP* 4.3 3.2 + - - -
573F THR* 6.2 0.2 - - - -
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Residues in contact with LEU 396 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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381F THR* 3.6 29.4 - - + -
388F LEU* 3.6 22.2 - - + -
392F ASP 2.9 17.4 + - - +
393F MET* 3.6 9.6 - - - +
394F GLN 3.3 0.2 - - - -
395F HIS* 1.3 77.4 - - - +
397F VAL* 1.3 56.8 + - - +
399F GLN 3.3 0.5 + - - -
400F THR* 2.9 36.1 + - + +
434F MET* 3.7 15.5 - - + +
437F LEU* 3.5 33.2 - - + -
438F ALA* 3.9 11.2 - - + +
441F TRP* 3.5 28.7 - - + -
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Residues in contact with VAL 397 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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315F LEU* 4.0 17.9 - - + -
317F ILE* 5.8 1.6 - - + -
337F LEU* 4.1 19.5 - - + +
338F ALA* 3.5 31.2 - - + -
378F ILE* 5.3 4.0 - - + -
393F MET* 3.1 16.5 + - + +
394F GLN 3.6 6.7 - - - +
395F HIS 3.2 0.2 - - - -
396F LEU* 1.3 73.5 - - - +
398F VAL* 1.3 68.9 + - - +
400F THR* 4.2 0.4 - - - -
401F SER* 2.7 34.4 + - - +
429F LEU* 3.7 9.6 - - + -
434F MET* 3.8 25.1 - - + -
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Residues in contact with VAL 398 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337F LEU* 3.8 25.4 - - + -
394F GLN 3.0 17.7 + - - +
395F HIS 3.6 6.7 - - - +
397F VAL* 1.3 77.9 - - - +
399F GLN* 1.3 63.8 + - + +
401F SER 4.1 5.2 + - - +
418F ARG* 3.6 42.1 - - - +
426F TYR* 3.8 39.3 - - + +
539F TRP* 3.8 30.3 - - + -
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Residues in contact with GLN 399 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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395F HIS* 2.9 23.1 + - - +
396F LEU 3.9 2.9 - - - +
398F VAL* 1.3 79.7 - - + +
400F THR* 1.3 59.3 + - - +
401F SER 4.7 2.1 - - - +
418F ARG* 3.8 26.0 + - - +
437F LEU* 3.6 24.5 - - + +
441F TRP* 3.7 29.6 - - - -
483F ARG* 4.6 9.7 - - - +
539F TRP* 6.2 0.2 - - - +
540F ASP* 4.5 12.0 + - - +
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Residues in contact with THR 400 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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396F LEU 2.9 22.9 + - - +
397F VAL* 4.0 1.0 + - - -
399F GLN* 1.3 79.0 - - - +
401F SER* 1.3 64.9 + - - +
402F LYS* 3.0 27.0 + - - +
430F ASP* 3.6 8.2 + - - +
433F ALA* 3.8 35.4 - - + +
434F MET* 3.2 24.3 - - - +
437F LEU* 3.7 24.2 - - + -
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Residues in contact with SER 401 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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338F ALA* 3.7 1.7 - - - +
397F VAL* 2.7 26.6 + - - +
398F VAL 4.1 4.0 + - - +
399F GLN 3.6 3.3 - - - +
400F THR* 1.3 79.6 + - - +
402F LYS* 1.3 63.5 + - - +
403F PRO* 3.7 5.2 - - - +
426F TYR* 3.3 29.6 - - - +
427F GLY 3.9 8.1 - - - -
428F LEU 3.3 10.5 - - - -
429F LEU* 3.3 27.7 - - - +
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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