Contacts of the helix formed by residues 424 - 436 (chain B) in PDB entry 2EZT
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 VAL 424 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64B MET* 4.0 16.4 - - + +
71B LYS* 5.4 1.6 - - - +
96B ASP* 4.5 7.4 - - - +
391B SER* 3.4 4.0 + - - -
392B ILE 3.4 22.4 - - - +
393B ASP* 3.9 7.4 - - - -
394B VAL* 4.3 0.7 - - + -
415B THR* 4.0 4.0 - - - +
416B SER* 3.8 24.0 - - - +
421B THR* 3.5 40.6 - - + +
423B GLY* 1.3 76.2 - - - +
425B GLY* 1.3 66.5 + - - +
426B ILE 3.4 0.7 - - - -
427B PRO* 3.6 7.4 - - + -
428B GLY* 2.9 22.7 + - - -
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Residues in contact with GLY 425 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
391B SER* 2.7 27.0 + - - -
393B ASP* 2.8 29.7 + - - -
424B VAL* 1.3 79.1 - - - +
426B ILE* 1.3 60.7 + - - +
429B ALA* 3.2 8.7 + - - +
443B ASN* 3.1 23.6 - - - +
445B ALA* 4.9 0.4 - - - -
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Residues in contact with ILE 426 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
393B ASP* 4.7 0.4 + - - -
423B GLY 3.9 1.0 + - - -
425B GLY* 1.3 74.1 - - - +
427B PRO* 1.4 67.1 - - + +
429B ALA* 3.2 5.2 + - - +
430B ILE* 3.0 47.7 + - + +
443B ASN* 3.5 22.9 - - - +
450B ALA* 3.9 19.3 - - + +
453B THR* 3.4 34.3 - - - +
454B MET* 3.9 6.5 - - - -
456B ASP* 3.8 24.7 - - + +
457B LEU* 3.9 21.1 - - + +
460B GLN* 4.0 10.1 + - - +
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Residues in contact with PRO 427 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61B VAL* 3.4 42.2 - - + +
64B MET* 3.6 29.2 - - + -
65B ALA* 3.5 15.6 - - + +
423B GLY 3.0 27.4 - - - +
424B VAL 3.4 7.6 - - - +
426B ILE* 1.4 92.9 - - + +
428B GLY* 1.3 54.6 + - - +
430B ILE* 3.3 5.4 + - + +
431B ALA* 2.9 25.8 + - - +
453B THR* 4.1 2.9 - - - +
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Residues in contact with GLY 428 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B MET 5.2 0.4 + - - -
68B ALA* 3.7 19.5 - - - -
391B SER* 3.1 20.4 - - - -
414B ILE* 4.0 10.4 - - - +
424B VAL* 2.9 12.6 + - - -
427B PRO* 1.3 77.2 - - - +
429B ALA* 1.3 56.2 + - - +
431B ALA* 3.5 2.6 + - - +
432B ALA* 2.9 28.2 + - - +
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Residues in contact with ALA 429 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
391B SER* 3.3 6.0 + - - -
425B GLY 3.2 13.2 + - - +
426B ILE 3.2 9.1 + - - +
427B PRO 3.2 0.6 - - - -
428B GLY* 1.3 74.3 - - - +
430B ILE* 1.3 59.3 + - - +
433B LYS* 3.0 31.0 + - - +
441B VAL* 3.6 18.2 - - + +
443B ASN* 3.8 9.4 - - + -
460B GLN* 4.4 0.7 - - - +
467B VAL* 3.5 34.7 - - + +
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Residues in contact with ILE 430 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B TYR* 4.3 13.0 - - + -
54B ILE* 4.9 1.6 - - + -
56B VAL* 6.0 0.9 - - + -
61B VAL* 4.2 10.5 - - + -
65B ALA* 4.8 1.8 - - + -
426B ILE* 3.0 29.3 + - + +
427B PRO* 3.3 11.9 + - + +
429B ALA* 1.3 74.6 - - - +
431B ALA* 1.3 61.5 + - - +
433B LYS* 3.3 1.9 + - - +
434B LEU* 3.0 37.4 + - + +
456B ASP 3.7 22.9 - - - +
459B THR* 4.1 20.9 - - + -
460B GLN* 3.7 20.6 - - + +
465B LEU* 3.7 22.9 - - + +
467B VAL* 4.8 1.6 - - - -
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Residues in contact with ALA 431 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B TYR* 3.6 12.8 - - - +
65B ALA 3.3 26.0 - - - +
68B ALA* 3.7 16.6 - - + -
69B ASP* 3.5 12.8 - - - +
72B LEU* 4.2 0.9 - - + -
427B PRO 2.9 15.8 + - - +
430B ILE* 1.3 76.6 - - - +
432B ALA* 1.3 63.3 + - - +
434B LEU* 3.2 3.1 + - - +
435B ASN* 2.9 30.0 + - - -
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Residues in contact with ALA 432 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B LEU* 3.4 21.5 - - + +
389B ILE* 3.7 25.4 - - + -
391B SER* 5.7 0.4 - - - -
414B ILE* 5.6 0.4 - - + -
428B GLY 2.9 18.5 + - - +
429B ALA* 3.7 0.4 - - - +
431B ALA* 1.3 76.7 - - - +
433B LYS* 1.3 57.3 + - - +
435B ASN 3.5 0.2 + - - -
436B TYR* 2.9 35.9 + - - +
441B VAL* 3.7 20.4 - - + +
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Residues in contact with LYS 433 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
429B ALA 3.0 18.5 + - - +
430B ILE 4.0 2.2 - - - +
432B ALA* 1.3 73.0 - - - +
434B LEU* 1.3 66.4 + - - +
436B TYR 4.0 8.7 - - - +
437B PRO* 3.2 39.7 + - + +
438B GLU 5.2 0.2 - - - -
439B ARG 2.5 29.0 + - - +
440B GLN* 4.1 2.4 - - - +
441B VAL* 3.8 19.5 - - + +
465B LEU* 3.9 23.0 - - + +
466B PRO* 3.6 54.6 + - + +
467B VAL* 4.3 3.1 - - + -
533B ALA 5.1 3.0 + - - -
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Residues in contact with LEU 434 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B ASP* 4.7 6.3 - - - +
28B HIS* 3.8 28.7 - - + +
30B TYR* 3.7 31.4 - - + +
52B HIS* 6.5 0.2 - - + -
54B ILE* 3.9 27.4 - - + -
430B ILE* 3.0 26.4 + - + +
431B ALA 3.2 4.2 + - - +
433B LYS* 1.3 79.0 - - - +
435B ASN* 1.3 60.1 + - - +
437B PRO* 3.9 8.1 - - - +
463B TYR* 5.3 2.0 - - + -
465B LEU* 3.7 25.8 - - + -
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Residues in contact with ASN 435 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B ASP* 5.8 1.1 - - - +
28B HIS* 3.3 16.6 - - - -
69B ASP* 2.8 33.2 + - - +
72B LEU* 4.3 5.5 - - - +
73B THR* 3.6 26.6 + - + +
431B ALA 2.9 22.6 + - - +
434B LEU* 1.3 75.8 - - - +
436B TYR* 1.3 86.6 + - + +
437B PRO* 3.4 7.2 - - - +
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Residues in contact with TYR 436 (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 LEU* 3.3 39.1 + - + -
73B THR* 3.7 14.8 - - + +
389B ILE* 3.4 24.7 - - + -
412B ARG* 4.6 4.7 + - + -
432B ALA* 2.9 18.9 + - - +
433B LYS* 3.5 6.4 - - - +
435B ASN* 1.3 96.4 - - + +
437B PRO* 1.3 63.3 - - - +
438B GLU 2.9 7.3 + - - +
439B ARG* 3.0 56.7 + - + +
441B VAL* 4.8 0.2 - - - +
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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