Contacts of the helix formed by residues 413 - 424 (chain D) in PDB entry 5H2U
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 PRO 413 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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286D VAL* 4.2 15.7 - - + -
290D LEU* 4.5 11.0 - - + -
381D PHE* 3.9 18.2 - - + -
411D GLU 3.5 7.4 - - - +
412D CYS* 1.3 86.5 - - - +
414D PRO* 1.3 64.7 - - + +
415D SER* 4.4 5.4 - - - +
416D VAL* 2.8 43.6 + - + +
417D HIS 3.2 8.5 + - - -
444D PHE* 5.6 4.5 - - + -
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Residues in contact with PRO 414 (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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186B ARG* 5.9 4.5 - - - +
211B LYS* 3.8 26.5 - - - +
408D CYS* 4.6 6.3 - - - -
412D CYS 3.2 7.1 - - - +
413D PRO* 1.3 83.6 - - + +
415D SER* 1.3 56.5 + - - +
417D HIS* 3.3 9.3 + - + +
418D LYS* 3.0 42.6 + - - +
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Residues in contact with SER 415 (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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413D PRO* 3.1 4.9 - - - +
414D PRO* 1.3 76.0 - - - +
416D VAL* 1.3 65.5 + - - +
418D LYS* 3.5 11.6 + - - +
419D LEU* 3.3 19.9 + - - +
440D ARG* 4.2 9.0 + - - +
444D PHE* 3.3 36.2 - - - -
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Residues in contact with VAL 416 (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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290D LEU* 3.7 29.2 - - + -
377D LEU* 4.7 9.2 - - + -
381D PHE* 3.8 20.0 - - + -
412D CYS* 3.8 16.6 - - - -
413D PRO* 2.8 28.7 + - + +
415D SER* 1.3 73.3 - - - +
417D HIS* 1.3 57.4 + - - +
419D LEU* 3.0 11.7 + - + +
420D MET* 3.0 33.2 + - + +
441D LEU* 4.6 10.5 - - + -
444D PHE* 4.5 17.0 - - + -
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Residues in contact with HIS 417 (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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213B ARG* 6.2 0.9 - - - -
406D MET 3.0 24.4 + - - -
407D PRO* 3.5 2.6 + - + -
408D CYS* 3.3 55.3 + - + +
409D PRO* 4.2 1.3 - - + -
412D CYS* 3.7 5.0 - - - -
413D PRO 3.2 5.1 + - - -
414D PRO 3.3 7.8 + - - +
416D VAL* 1.3 74.3 - - - +
418D LYS* 1.3 65.5 + - - +
420D MET* 3.2 29.3 + - + +
421D LEU* 3.0 51.7 + - + +
424D TRP* 4.4 1.4 - + - -
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Residues in contact with LYS 418 (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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414D PRO* 3.0 32.7 + - - +
415D SER* 3.8 10.6 - - - +
416D VAL 3.3 0.2 - - - -
417D HIS* 1.3 76.4 + - + +
419D LEU* 1.3 60.8 + - - +
421D LEU* 3.4 19.5 - - + +
422D THR* 3.3 24.9 + - - +
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Residues in contact with LEU 419 (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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377D LEU* 5.7 4.7 - - + -
415D SER 3.3 10.1 + - - +
416D VAL* 3.0 12.4 + - + +
418D LYS* 1.3 77.3 - - - +
420D MET* 1.3 64.8 + - - +
422D THR* 2.6 37.7 + - + +
423D CYS* 3.1 10.5 + - - -
432D PRO* 5.0 3.1 - - + -
437D LEU* 3.7 25.6 - - + +
440D ARG* 3.8 39.0 - - + -
441D LEU* 4.0 28.9 - - + -
444D PHE* 5.0 3.6 - - + -
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Residues in contact with MET 420 (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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374D GLY* 3.8 3.4 - - - +
377D LEU* 3.7 36.8 - - + +
378D HIS* 3.7 31.9 - - + +
407D PRO 5.7 0.2 - - - +
409D PRO* 4.5 3.8 - - + -
412D CYS* 4.1 14.8 - - - -
416D VAL* 3.0 14.5 + - - +
417D HIS* 3.4 34.5 - - + +
419D LEU* 1.3 74.5 - - - +
421D LEU* 1.3 58.0 + - - +
423D CYS* 3.0 28.3 + - - +
424D TRP* 3.1 50.2 + - + -
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Residues in contact with LEU 421 (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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405D ARG* 4.3 17.6 + - + -
406D MET 4.4 1.1 - - - +
417D HIS* 3.0 48.7 + - + +
418D LYS* 3.4 22.2 - - + +
420D MET* 1.3 75.3 - - - +
422D THR* 1.3 60.6 + - + +
424D TRP* 3.3 32.2 + - + +
425D CYS* 3.5 11.6 + - - -
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Residues in contact with THR 422 (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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418D LYS 3.3 15.9 + - - +
419D LEU* 2.6 28.7 + - + +
421D LEU* 1.3 71.5 - - - +
423D CYS* 1.3 63.5 + - - +
424D TRP 3.1 2.3 + - - -
425D CYS* 3.4 19.5 - - - -
430D GLN 5.3 1.6 - - - -
431D ARG* 3.3 16.3 - - - +
432D PRO* 3.4 28.3 - - - +
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Residues in contact with CYS 423 (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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370D VAL* 3.3 38.4 - - - +
371D TRP* 3.3 13.0 - - - -
373D PHE* 4.5 3.1 - - - -
374D GLY* 4.0 19.7 - - - -
377D LEU* 5.0 2.0 - - - -
419D LEU 3.1 18.2 + - - -
420D MET* 3.0 13.6 + - - +
422D THR* 1.3 77.5 + - - +
424D TRP* 1.3 57.8 + - + +
425D CYS 3.4 0.4 - - - -
431D ARG* 3.2 21.9 + - - -
432D PRO* 4.5 0.4 - - - -
437D LEU* 3.8 27.4 - - - -
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Residues in contact with TRP 424 (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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371D TRP* 3.1 50.6 + + + -
374D GLY* 3.3 25.2 - - - -
375D ILE* 3.5 25.8 - - + +
388D TYR* 5.6 1.8 - - - -
405D ARG* 2.8 53.8 + - + +
406D MET* 4.1 36.3 - - + -
417D HIS* 4.4 0.9 - - - -
420D MET* 3.1 40.5 + - + +
421D LEU* 3.3 39.0 + - + +
422D THR 3.1 1.2 - - - -
423D CYS* 1.3 82.1 - - + +
425D CYS* 1.3 64.4 + - - +
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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