Contacts of the helix formed by residues 393 - 407 (chain D) in PDB entry 1U3Q
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 GLN 393 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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345D TRP* 4.0 2.5 - - - -
391D LYS* 2.9 27.4 + - - +
392D LEU* 1.3 79.2 + - - +
394D HIS* 1.3 67.9 + - - +
395D LYS* 4.4 5.2 - - + +
396D GLU* 2.9 42.2 + - + +
397D TYR* 2.9 12.1 + - - +
440D VAL* 5.6 2.2 - - + -
454D ARG* 4.5 2.7 - - - +
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Residues in contact with HIS 394 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273D LEU* 3.5 32.3 - - + +
276D GLU* 4.5 7.2 + - + +
345D TRP* 3.3 48.2 + + + -
393D GLN* 1.3 72.3 - - - +
395D LYS* 1.3 62.8 + - + +
397D TYR* 3.2 18.7 - + - +
398D LEU* 3.0 36.1 + - + +
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Residues in contact with LYS 395 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269D VAL* 4.0 25.5 - - + +
270D LEU* 4.9 14.8 - - - +
273D LEU* 5.3 11.0 - - + -
393D GLN* 3.2 4.2 - - + +
394D HIS* 1.3 81.9 - - + +
396D GLU* 1.3 64.6 + - + +
397D TYR 3.2 0.4 - - - -
398D LEU* 3.6 13.0 + - + +
399D CYS* 3.4 27.2 + - - -
439D TRP* 5.5 9.0 - - + -
440D VAL* 3.9 27.9 - - + +
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Residues in contact with GLU 396 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
392D LEU* 3.7 11.4 - - + +
393D GLN* 2.9 35.6 + - + +
395D LYS* 1.3 77.2 - - - +
397D TYR* 1.3 53.5 - - - +
399D CYS* 3.2 2.9 + - - +
400D VAL* 2.8 41.5 + - - +
437D LEU* 4.1 19.1 - - + -
440D VAL* 3.9 19.3 - - + -
441D ILE* 3.6 14.8 - - + +
454D ARG* 2.6 50.5 + - - -
458D LEU* 4.2 7.9 - - + +
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Residues in contact with TYR 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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276D GLU* 3.3 23.0 + - - -
341D MET* 3.8 31.6 - - + -
342D GLY* 3.8 13.3 + - - -
345D TRP* 3.4 46.7 - + + -
346D ARG* 5.4 1.4 + - - -
392D LEU* 4.2 15.4 - - + +
393D GLN 2.9 11.3 + - - +
394D HIS* 3.2 31.0 - + - +
396D GLU* 1.3 77.1 - - - +
398D LEU* 1.3 60.0 + - + +
400D VAL* 3.8 5.2 - - - +
401D LYS* 2.9 66.0 + - - +
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Residues in contact with LEU 398 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269D VAL* 4.0 11.7 - - + +
272D LEU* 3.6 26.6 - - + +
273D LEU* 3.4 44.0 - - + +
276D GLU* 3.2 44.2 - - + +
312D TRP* 5.4 1.3 + - - +
394D HIS* 3.0 25.0 + - + +
395D LYS* 3.8 15.7 - - + +
396D GLU 3.2 0.4 - - - -
397D TYR* 1.3 82.0 - - + +
399D CYS* 1.3 61.8 + - - +
401D LYS* 3.7 5.7 - - + +
402D ALA* 3.3 16.8 + - - +
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Residues in contact with CYS 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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269D VAL* 4.1 13.5 - - - -
272D LEU* 4.0 13.5 - - - -
395D LYS 3.4 15.0 + - - +
396D GLU 3.2 7.2 + - - +
398D LEU* 1.3 77.0 - - - +
400D VAL* 1.3 60.8 + - - +
402D ALA 3.4 1.0 + - - -
403D MET* 3.0 34.7 + - - +
433D VAL* 3.3 8.8 - - + +
436D ALA* 4.0 15.5 - - - -
437D LEU* 3.7 44.2 - - + +
440D VAL* 4.6 1.1 - - - -
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Residues in contact with VAL 400 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341D MET* 4.2 19.7 - - + -
387D PHE* 5.6 3.1 - - + -
392D LEU* 5.1 5.4 - - + -
396D GLU* 2.8 28.4 + - + +
397D TYR* 3.8 7.0 - - - +
399D CYS* 1.3 70.2 - - - +
401D LYS* 1.3 64.5 + - - +
403D MET* 3.2 9.5 + - - +
404D ILE* 2.9 24.0 + - + +
437D LEU* 4.3 17.5 - - + -
458D LEU* 4.6 21.5 - - + +
459D LEU* 5.9 1.8 - - + -
462D LEU* 3.6 34.3 - - + -
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Residues in contact with LYS 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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276D GLU* 2.4 40.2 + - - +
277D PRO* 3.7 16.4 - - - +
312D TRP* 3.5 37.8 - - + +
338D VAL* 4.3 28.0 - - + +
341D MET* 4.8 6.7 - - + -
342D GLY* 5.4 0.7 - - - -
397D TYR* 2.9 56.2 + - + +
398D LEU* 3.7 5.8 - - - +
400D VAL* 1.3 79.7 - - - +
402D ALA* 1.3 60.8 + - - +
404D ILE* 3.4 12.3 + - - +
405D LEU 3.4 13.9 + - - -
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Residues in contact with ALA 402 (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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272D LEU* 4.2 14.8 - - + -
312D TRP* 3.8 13.2 - - + -
316D ILE* 4.3 17.0 - - + -
398D LEU 3.3 10.9 + - - +
399D CYS 3.8 6.5 - - - +
400D VAL 3.3 0.2 - - - -
401D LYS* 1.3 77.5 - - - +
403D MET* 1.3 60.3 + - - +
405D LEU* 3.1 6.3 + - - +
406D LEU* 2.9 31.1 + - + +
433D VAL* 3.9 20.4 - - + -
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Residues in contact with MET 403 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
460B MET* 3.7 16.2 - - + -
399D CYS 3.0 29.2 + - - +
400D VAL* 3.2 8.0 + - - +
402D ALA* 1.3 72.8 - - - +
404D ILE* 1.3 66.4 + - - +
406D LEU* 4.6 0.7 - - - -
407D ASN* 2.9 30.8 + - - +
430D LEU* 4.1 13.2 - - + +
433D VAL* 3.5 17.9 - - + -
434D THR* 3.4 32.5 - - + +
437D LEU* 3.4 33.7 - - + -
459D LEU* 3.5 30.1 - - + -
462D LEU* 5.3 6.1 - - + -
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Residues in contact with ILE 404 (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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334D CYS* 4.0 5.6 - - + +
337D GLU* 3.2 42.5 - - + +
338D VAL* 4.3 8.1 - - + +
341D MET* 3.9 34.8 - - + -
400D VAL 2.9 21.0 + - - +
401D LYS* 3.5 9.9 - - - +
403D MET* 1.3 77.5 - - - +
405D LEU* 1.3 65.2 + - - +
407D ASN* 4.1 2.4 - - - +
408D SER* 3.6 19.2 + - - -
462D LEU* 4.0 33.8 - - + +
465D VAL* 4.5 7.4 - - + -
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Residues in contact with LEU 405 (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 TRP* 3.9 20.2 - - + -
313D ALA* 3.7 20.6 - - + -
316D ILE* 3.4 31.0 - - + -
319D PHE* 4.1 12.8 - - + -
330D LEU* 3.6 25.2 - - + +
331D LEU* 3.9 19.1 - - + -
334D CYS* 3.7 24.5 - - - -
338D VAL* 4.8 0.9 - - + +
401D LYS 3.4 1.4 + - - -
402D ALA 3.1 8.4 + - - +
404D ILE* 1.3 80.7 - - - +
406D LEU* 1.3 63.8 + - + +
408D SER* 2.7 22.7 + - - -
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Residues in contact with LEU 406 (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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316D ILE* 4.3 9.4 - - + -
319D PHE* 4.5 13.9 - - + -
322D LEU* 4.8 0.4 - - + -
330D LEU* 4.4 12.4 - - + +
402D ALA 2.9 17.7 + - - +
403D MET 3.2 0.2 + - - -
405D LEU* 1.3 81.7 - - + +
407D ASN* 1.3 57.9 + - - +
408D SER 3.5 0.8 + - - -
409D SER 4.4 1.2 - - - +
426D LEU* 3.6 44.5 - - + +
429D LEU* 3.6 37.0 - - + -
430D LEU* 3.9 34.6 - - + +
433D VAL* 3.7 23.8 - - + -
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Residues in contact with ASN 407 (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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386B ARG* 3.9 9.1 - - - +
460B MET* 2.9 45.4 + - - +
463B SER* 4.0 11.4 + - - -
464B HIS* 3.0 37.9 + - - -
403D MET 2.9 17.2 + - - +
404D ILE* 4.1 3.8 - - - +
405D LEU 3.3 0.2 - - - -
406D LEU* 1.3 75.9 - - - +
408D SER* 1.3 56.9 + - - +
409D SER 3.1 7.8 + - - -
430D LEU* 3.5 21.3 - - + +
466D ARG* 5.1 2.8 + - - -
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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
------------------------------------------------------------
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