Contacts of the helix formed by residues 413 - 430 (chain B) in PDB entry 5T5I
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 SER 413 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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93B GLU* 5.9 0.7 - - - -
383B ALA* 4.3 12.0 - - - +
389B ALA* 4.7 17.9 - - - -
411B LEU 3.9 0.8 + - - -
412B LEU* 1.3 76.9 - - - +
414B ASP* 1.3 63.9 + - - +
415B ARG* 3.6 15.3 + - - +
416B GLU* 3.0 37.4 + - - +
417B ILE* 3.0 21.9 + - - +
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Residues in contact with ASP 414 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91B CYS 5.1 1.2 - - - +
92B THR* 2.7 35.1 + - - +
93B GLU* 5.7 0.2 - - - +
96B ALA* 3.8 7.4 - - + -
341B ILE* 3.9 14.6 - - + +
342B ALA* 5.2 3.0 - - - +
365B ILE* 3.4 17.2 - - - +
382B PRO* 3.3 27.8 - - - +
383B ALA 4.5 5.2 + - - +
385B VAL* 4.3 10.1 - - + +
413B SER* 1.3 72.0 - - - +
415B ARG* 1.3 58.0 + - - +
417B ILE* 3.3 8.1 + - - +
418B LEU* 2.9 37.1 + - - +
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Residues in contact with ARG 415 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93B GLU* 3.9 18.5 + - - +
95B GLU* 3.2 42.9 + - + +
96B ALA* 3.7 15.0 - - - +
99B VAL* 4.5 7.1 - - + +
413B SER* 3.2 10.0 + - - +
414B ASP* 1.3 79.4 - - - +
416B GLU* 1.4 90.2 + - - +
418B LEU* 3.4 3.3 + - - +
419B GLU* 2.9 63.6 + - - +
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Residues in contact with GLU 416 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
411B LEU 4.8 0.7 - - - +
412B LEU* 3.7 27.8 - - + +
413B SER* 3.0 42.1 + - - +
415B ARG* 1.4 107.1 + - - +
417B ILE* 1.4 63.3 + - - +
419B GLU* 3.4 5.6 + - - +
420B ARG* 3.1 34.5 + - - +
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Residues in contact with ILE 417 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B TYR* 4.2 3.1 - - + -
71B ILE* 4.3 17.7 - - + +
365B ILE* 4.0 30.3 - - + -
380B ILE* 3.8 36.6 - - + -
381B PRO 4.0 7.2 - - - +
382B PRO* 3.9 17.9 - - + -
412B LEU* 3.9 31.6 - - + +
413B SER 3.0 18.3 + - - +
414B ASP* 3.7 6.5 - - - +
416B GLU* 1.4 74.6 - - - +
418B LEU* 1.3 57.4 + - - +
420B ARG* 3.4 4.2 + - - +
421B LEU* 3.0 29.2 + - + +
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Residues in contact with LEU 418 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89B TRP* 3.8 19.5 - - + -
96B ALA* 3.3 34.5 - - + +
99B VAL* 3.6 17.8 - - + +
100B GLY* 4.5 2.0 - - - +
103B LEU* 4.2 16.0 - - + +
339B MET* 4.0 26.7 - - + -
341B ILE* 3.8 12.8 - - + -
365B ILE* 4.1 15.7 - - + -
414B ASP 2.9 21.2 + - - +
415B ARG 3.9 2.2 - - - +
417B ILE* 1.3 72.7 - - - +
419B GLU* 1.3 59.5 + - - +
421B LEU* 3.3 6.7 + - + +
422B LEU* 2.8 29.8 + - - +
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Residues in contact with GLU 419 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95B GLU* 4.5 5.0 - - - +
99B VAL* 4.0 22.2 - - + +
415B ARG* 2.9 57.2 + - - +
416B GLU* 3.4 6.7 + - - +
418B LEU* 1.3 74.6 - - - +
420B ARG* 1.3 62.2 + - + +
422B LEU* 3.4 8.1 + - + +
423B GLU* 3.1 22.7 + - - +
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Residues in contact with ARG 420 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B TYR* 4.5 9.3 - - - +
68B ASP* 4.2 17.8 + - - -
71B ILE* 4.0 25.5 - - + +
412B LEU* 3.7 39.0 - - - +
416B GLU* 3.1 19.1 + - - +
417B ILE 3.7 6.7 - - - +
419B GLU* 1.3 73.3 - - + +
421B LEU* 1.3 65.4 + - - +
423B GLU* 3.4 10.4 + - - +
424B LYS* 3.2 27.8 + - + +
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Residues in contact with LEU 421 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B ILE* 3.8 21.2 - - + +
74B ALA* 3.8 13.5 - - + -
75B ALA* 3.6 34.1 - - - +
78B LEU* 3.9 8.7 - - + -
103B LEU* 3.6 18.8 - - + -
339B MET* 3.5 31.2 - - - -
363B ILE* 6.1 0.9 - - + -
365B ILE* 4.9 6.3 - - + -
380B ILE* 5.9 2.0 - - + -
417B ILE* 3.0 18.9 + - + +
418B LEU* 3.5 11.7 - - + +
420B ARG* 1.3 77.9 - - - +
422B LEU* 1.4 55.3 + - - +
424B LYS* 3.3 3.2 + - - +
425B VAL* 2.9 35.3 + - + +
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Residues in contact with LEU 422 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99B VAL* 4.4 13.2 - - + -
102B GLU* 3.7 31.4 - - + +
103B LEU* 3.9 35.8 - - + +
106B GLU* 4.0 15.0 - - + -
418B LEU 2.8 18.2 + - - +
419B GLU* 3.6 8.5 - - + +
420B ARG 3.4 0.2 - - - -
421B LEU* 1.4 75.5 - - - +
423B GLU* 1.4 61.5 + - - +
425B VAL* 4.0 0.7 - - - +
426B ARG* 3.1 57.8 + - - +
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Residues in contact with GLU 423 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
419B GLU 3.1 13.4 + - - +
420B ARG* 3.7 11.8 - - - +
421B LEU 3.4 0.2 - - - -
422B LEU* 1.4 74.8 - - - +
424B LYS* 1.4 69.2 + - + +
426B ARG* 3.5 13.2 - - - +
427B GLU* 3.1 29.3 + - - +
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Residues in contact with LYS 424 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71B ILE* 4.3 14.6 - - + +
72B ASP* 3.4 31.9 + - - +
75B ALA* 3.4 21.8 - - + -
420B ARG* 3.2 18.7 + - + +
421B LEU* 3.8 1.3 - - - +
423B GLU* 1.4 81.9 - - - +
425B VAL* 1.3 61.5 + - - +
427B GLU* 3.1 37.4 + - - +
428B TYR* 2.9 36.4 + - - -
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Residues in contact with VAL 425 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75B ALA* 3.8 29.6 - - - +
78B LEU* 4.0 14.4 - - + -
79B ALA* 4.6 7.6 - - + -
103B LEU* 4.0 21.5 - - + -
106B GLU* 4.0 19.1 - - + -
107B ALA* 4.5 14.6 - - + -
421B LEU 2.9 20.8 + - - +
422B LEU 4.0 3.6 - - - +
424B LYS* 1.3 73.1 - - - +
426B ARG* 1.3 53.3 + - - +
428B TYR* 3.2 6.3 + - - +
429B LYS* 2.8 44.2 + - + +
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Residues in contact with ARG 426 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102B GLU* 2.8 36.4 + - - +
106B GLU* 3.3 38.8 + - - +
422B LEU* 3.1 43.7 + - - +
423B GLU* 3.5 10.1 - - - +
425B VAL* 1.3 76.6 - - - +
427B GLU* 1.3 60.7 + - - +
429B LYS* 3.5 2.5 + - - +
430B ALA* 3.1 23.6 + - - +
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Residues in contact with GLU 427 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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423B GLU* 3.1 17.0 + - - +
424B LYS* 3.1 44.1 + - - +
426B ARG* 1.3 76.1 - - - +
428B TYR* 1.4 66.2 + - + +
430B ALA* 3.3 22.2 + - - +
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Residues in contact with TYR 428 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72B ASP* 2.8 49.3 + - - -
75B ALA* 4.0 8.1 - - + -
76B LYS* 3.9 40.0 - - + +
79B ALA* 3.5 25.1 - - + +
424B LYS* 2.9 30.8 + - - +
425B VAL 3.8 0.4 - - - +
427B GLU* 1.4 81.1 - - + +
429B LYS* 1.3 61.2 + - - +
430B ALA 3.5 4.3 + - - -
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Residues in contact with LYS 429 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78B LEU 5.1 0.2 + - - -
79B ALA* 3.2 32.8 + - + +
81B SER 5.0 0.6 + - - -
106B GLU* 3.6 36.6 - - - +
107B ALA* 4.1 18.9 + - - +
425B VAL* 2.8 32.7 + - + +
426B ARG 3.8 4.5 - - - +
428B TYR* 1.3 72.5 - - - +
430B ALA* 1.3 60.8 + - - +
43C ASN* 4.7 11.3 + - - +
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Residues in contact with ALA 430 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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426B ARG 3.1 17.3 + - - +
427B GLU* 3.6 15.3 - - - +
428B TYR 3.3 5.3 - - - -
429B LYS* 1.3 79.9 - - - +
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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