Contacts of the helix formed by residues 389 - 401 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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282D ARG* 4.0 3.0 + - - -
284D GLY 5.5 0.9 - - - +
285D LEU* 3.2 35.0 - - + +
288D ILE* 4.5 0.2 - - - +
387D ASN 4.3 1.1 - - - +
388D LEU* 1.3 76.4 - - - +
390D TRP* 1.3 69.8 + - - +
391D ARG* 3.4 9.3 + - - +
392D ASP* 2.8 38.9 + - - +
393D MET* 3.1 21.0 + - - +
443D THR* 3.9 16.8 - - + -
444D VAL* 4.5 3.3 - - + +
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Residues in contact with TRP 390 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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278D VAL* 3.3 43.9 + - + +
282D ARG* 4.0 1.0 - - - +
285D LEU 2.9 16.7 + - - -
286D GLY 3.9 4.7 - - - +
287D SER 3.8 21.8 - - - +
288D ILE* 3.7 14.2 - - + +
312D ILE* 3.6 26.7 - - + -
313D TYR* 4.1 20.2 - + - +
315D LEU* 5.6 1.2 - - - +
389D THR* 1.3 77.5 - - - +
391D ARG* 1.3 95.9 + - + +
393D MET* 3.6 4.5 + - - +
394D GLN* 3.5 41.0 + - - +
447D GLN* 3.7 20.4 - - - -
486D HIS* 4.5 5.2 - + - -
601D FMT 4.0 18.6 + - - -
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Residues in contact with ARG 391 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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389D THR* 3.1 6.6 + - - +
390D TRP* 1.3 121.1 - - + +
392D ASP* 1.3 65.9 + - - +
393D MET 3.1 1.6 - - - -
394D GLN* 3.1 8.4 + - - +
395D HIS* 3.0 30.6 + - + -
444D VAL* 3.5 18.3 + - + +
445D ALA 2.8 30.1 + - - -
446D PRO* 4.1 2.0 - - - +
447D GLN* 3.2 36.4 - - - +
485D GLU* 2.9 40.2 + - - +
486D HIS* 5.3 4.7 - - + -
539D TRP* 4.8 0.8 - - + -
573D THR* 3.4 13.7 - - - +
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Residues in contact with ASP 392 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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388D LEU* 3.5 18.8 - - + +
389D THR* 2.8 40.1 + - - +
391D ARG* 1.3 75.3 - - - +
393D MET* 1.3 62.6 + - - +
395D HIS* 3.0 9.0 + - - +
396D LEU* 2.9 26.7 + - - +
441D TRP* 3.0 25.2 + - - +
443D THR* 3.4 18.9 + - - +
444D VAL* 3.0 32.6 + - - +
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Residues in contact with MET 393 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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288D ILE* 4.1 15.0 - - + -
315D LEU* 4.2 15.9 - - + -
378D ILE* 3.6 36.3 - - + +
381D THR* 3.9 12.1 - - + -
382D LEU* 3.8 28.7 - - + -
388D LEU* 3.9 19.5 - - + +
389D THR 3.1 8.4 + - - +
390D TRP 3.7 10.3 - - - +
391D ARG 3.1 0.2 - - - -
392D ASP* 1.3 80.3 - - - +
394D GLN* 1.3 61.2 + - - +
396D LEU* 3.3 7.2 + - - +
397D VAL* 3.2 22.7 + - + +
434D MET* 3.9 20.9 - - - -
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Residues in contact with GLN 394 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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312D ILE 3.0 22.3 + - - +
313D TYR 4.3 5.1 + - - -
314D THR 4.2 9.3 + - - +
315D LEU* 3.8 28.1 - - + +
337D LEU* 3.9 19.4 - - + +
390D TRP* 3.5 28.3 + - - +
391D ARG* 3.1 9.4 + - - +
393D MET* 1.3 74.1 - - - +
395D HIS* 1.3 66.3 + - - +
397D VAL* 3.3 3.7 + - - +
398D VAL* 3.0 29.7 + - - +
486D HIS* 2.7 29.3 + - - -
539D TRP* 3.8 14.8 - - + -
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Residues in contact with HIS 395 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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391D ARG* 3.0 29.0 + - + -
392D ASP 3.0 8.3 + - - +
394D GLN* 1.3 76.5 - - - +
396D LEU* 1.3 63.4 + - - +
398D VAL* 3.2 3.5 + - - +
399D GLN* 2.9 30.6 + - - +
441D TRP* 3.5 22.4 - + + -
444D VAL* 3.4 29.8 - - + +
483D ARG* 5.4 10.0 + - + -
485D GLU* 2.8 36.0 + - + +
539D TRP* 3.2 34.9 + + - +
540D ASP* 4.5 14.0 + - - -
573D THR* 6.1 0.7 - - + -
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Residues in contact with LEU 396 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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381D THR* 3.7 17.5 - - + -
388D LEU* 3.6 35.9 - - + -
392D ASP 2.9 16.7 + - - +
393D MET* 3.6 11.7 - - - +
394D GLN 3.3 0.2 - - - -
395D HIS* 1.3 77.2 - - - +
397D VAL* 1.3 56.6 + - - +
399D GLN 3.3 0.5 + - - -
400D THR* 2.9 35.9 + - + +
434D MET* 3.7 15.3 - - + +
437D LEU* 3.5 26.2 - - + -
438D ALA* 4.0 8.7 - - + +
441D TRP* 3.5 38.4 - - + -
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Residues in contact with VAL 397 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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315D LEU* 4.0 19.5 - - + -
317D ILE* 5.7 2.2 - - + -
337D LEU* 4.0 20.6 - - + +
338D ALA* 3.5 31.6 - - + -
378D ILE* 5.2 4.5 - - + -
393D MET* 3.2 15.6 + - + +
394D GLN 3.6 7.4 - - - +
396D LEU* 1.3 75.1 - - - +
398D VAL* 1.3 63.9 + - - +
401D SER* 2.7 35.1 + - - +
429D LEU* 3.7 9.6 - - + -
434D MET* 3.7 23.6 - - + -
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Residues in contact with VAL 398 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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337D LEU* 3.9 21.1 - - + -
394D GLN 3.0 15.4 + - - +
395D HIS 3.6 5.8 - - - +
397D VAL* 1.3 78.0 - - - +
399D GLN* 1.3 64.1 + - + +
400D THR 3.6 0.2 + - - -
401D SER 4.1 5.2 + - - +
418D ARG* 3.6 40.3 - - - +
426D TYR* 3.7 38.3 - - + +
539D TRP* 3.9 34.5 - - + -
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Residues in contact with GLN 399 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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395D HIS* 2.9 19.3 + - - +
396D LEU 3.9 2.5 - - - +
398D VAL* 1.3 81.0 - - + +
400D THR* 1.3 59.7 + - - +
401D SER 3.6 1.8 - - - +
418D ARG* 3.6 30.0 - - - +
437D LEU* 3.7 24.1 - - + +
441D TRP* 3.4 33.9 - - - -
483D ARG* 4.5 14.8 - - - +
540D ASP* 4.6 7.2 + - - +
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Residues in contact with THR 400 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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396D LEU* 2.9 23.2 + - - +
397D VAL* 4.0 1.0 + - - -
399D GLN* 1.3 77.5 - - - +
401D SER* 1.3 64.6 + - - +
402D LYS* 2.8 29.6 + - - +
430D ASP* 3.6 8.1 + - - +
433D ALA* 3.8 34.5 - - + +
434D MET* 3.2 24.6 - - - +
437D LEU* 3.5 27.1 - - + -
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Residues in contact with SER 401 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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338D ALA* 3.7 1.5 - - - +
397D VAL* 2.7 26.8 + - - +
398D VAL 4.1 4.2 + - - +
399D GLN 3.6 2.9 - - - +
400D THR* 1.3 79.3 + - - +
402D LYS* 1.3 62.4 + - - +
403D PRO* 3.7 5.2 - - - +
426D TYR* 3.4 33.5 - - - +
427D GLY 3.9 4.5 - - - -
428D LEU 3.3 11.2 - - - -
429D LEU* 3.5 27.3 - - - +
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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
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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