Contacts of the helix formed by residues 268 - 279 (chain A) in PDB entry 5MJU
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 TYR 268 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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84A PRO* 2.7 44.4 + - - +
87A LEU* 3.5 20.4 - - + +
88A LEU* 3.6 33.7 - - + -
91A MET* 3.7 29.4 - - + -
264A ILE 4.3 1.4 + - - +
265A ILE* 3.1 13.3 + - - +
267A TRP* 1.3 76.7 - - - +
269A ALA* 1.3 64.5 + - - +
270A PRO 3.4 0.2 - - - -
271A LEU* 3.1 39.3 + - + +
272A GLY* 3.2 7.7 + - - -
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Residues in contact with ALA 269 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54A THR* 4.4 7.2 - - + -
88A LEU* 3.7 17.9 - - + +
265A ILE 3.5 4.7 + - - +
266A MET* 3.3 20.6 + - + +
268A TYR* 1.3 74.7 - - - +
270A PRO* 1.4 60.8 - - + +
272A GLY 3.1 1.0 + - - -
273A ILE* 2.8 34.5 + - + +
334A GLN* 6.0 1.1 - - + +
338A THR* 4.2 23.8 - - + -
351A ILE* 6.0 2.7 - - + -
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Residues in contact with PRO 270 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A LEU* 3.8 22.4 - - + -
53A LEU* 3.9 41.1 - - + +
54A THR* 4.0 5.8 - - + -
57A ALA* 3.2 18.8 - - + +
267A TRP* 3.4 18.8 - - + +
268A TYR 3.5 0.2 - - - -
269A ALA* 1.4 91.0 - - + +
271A LEU* 1.4 61.9 + - + +
273A ILE* 4.8 0.4 - - + -
274A LEU* 3.2 23.8 + - - +
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Residues in contact with LEU 271 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84A PRO* 3.8 22.1 - - + +
267A TRP 5.7 0.2 - - - +
268A TYR* 3.1 33.2 + - + +
270A PRO* 1.4 78.4 - - + +
272A GLY* 1.3 57.1 + - - +
274A LEU* 4.0 5.8 - - - +
275A PHE* 3.0 41.6 + - + -
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Residues in contact with GLY 272 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A PRO 3.4 20.6 + - - -
85A GLY* 3.3 8.5 - - - -
88A LEU* 4.0 15.9 - - - -
268A TYR* 3.2 7.3 + - - -
269A ALA 3.1 5.4 + - - -
271A LEU* 1.3 74.9 - - - +
273A ILE* 1.4 53.2 + - - +
274A LEU 3.1 2.1 + - - -
275A PHE 3.2 2.3 + - - -
276A LEU* 2.8 35.4 + - - +
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Residues in contact with ILE 273 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A THR* 4.5 8.7 - - - +
57A ALA* 4.7 5.4 - - + -
58A VAL* 4.0 27.4 - - + +
88A LEU* 3.7 19.1 - - + -
269A ALA 2.8 25.5 + - - +
270A PRO* 4.3 2.7 - - + +
272A GLY* 1.4 69.9 - - - +
274A LEU* 1.4 62.7 + - - +
276A LEU* 3.9 6.1 - - + -
277A ILE* 3.4 24.5 + - + +
337A ILE* 4.2 11.4 - - + +
338A THR* 3.8 46.9 - - + +
341A GLY* 4.2 13.5 - - - -
342A THR* 4.1 7.9 - - + +
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Residues in contact with LEU 274 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57A ALA* 3.6 31.8 - - + +
60A LEU* 3.8 32.3 - - + +
61A GLY* 3.8 6.0 - - - +
64A LEU* 3.9 27.6 - - + -
81A PHE* 6.0 0.2 - - + -
270A PRO 3.2 16.5 + - - +
271A LEU* 4.0 9.2 - - - +
273A ILE* 1.4 78.2 - - - +
275A PHE* 1.4 72.3 + - + +
277A ILE* 3.7 3.1 - - - +
278A ALA* 2.8 38.8 + - + +
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Residues in contact with PHE 275 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64A LEU* 5.9 4.0 - - + -
81A PHE* 3.0 52.2 - + - +
82A ALA* 3.7 12.3 - - - +
84A PRO* 3.6 34.8 - - + -
85A GLY* 3.9 10.5 - - - +
271A LEU* 3.0 32.5 - - + -
272A GLY 3.2 2.2 + - - +
274A LEU* 1.4 91.9 - - + +
276A LEU* 1.4 58.6 + - - +
278A ALA* 3.9 7.2 - - - -
279A GLY* 3.2 21.4 + - - +
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Residues in contact with LEU 276 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82A ALA* 5.6 2.1 - - - +
85A GLY* 3.4 30.5 - - - +
88A LEU* 4.1 17.5 - - + -
89A MET* 3.8 25.6 - - + -
272A GLY 2.8 14.7 + - - +
273A ILE* 3.9 9.0 - - + +
274A LEU 3.2 0.4 - - - -
275A PHE* 1.4 75.0 - - - +
277A ILE* 1.4 58.6 + - - +
280A LYS* 3.4 33.7 + - + +
341A GLY 3.4 21.8 - - - +
342A THR* 4.1 17.5 - - - +
457A ARG* 3.8 8.6 + - - +
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Residues in contact with ILE 277 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57A ALA 4.8 1.8 - - - +
58A VAL* 3.6 26.2 - - + +
61A GLY* 3.6 28.0 - - - -
62A VAL* 3.8 11.9 - - + +
273A ILE* 3.4 19.2 + - + +
274A LEU 3.3 4.0 + - - +
276A LEU* 1.4 75.2 - - - +
278A ALA* 1.4 64.7 + - - +
279A GLY 3.4 0.4 - - - -
280A LYS* 3.9 4.9 - - - +
281A ILE* 3.3 35.0 + - + +
340A LEU 3.8 9.6 - - - +
341A GLY* 3.8 29.2 - - - -
457A ARG* 4.2 10.1 - - + +
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Residues in contact with ALA 278 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61A GLY* 3.3 23.8 - - - +
64A LEU* 4.7 4.3 - - + -
65A GLY* 3.4 16.2 - - - +
81A PHE* 3.7 23.4 - - + -
274A LEU* 2.8 25.0 + - + +
275A PHE* 4.0 2.2 - - - -
277A ILE* 1.4 76.5 - - - +
279A GLY* 1.3 60.9 + - - +
281A ILE* 3.6 4.3 - - - +
282A VAL* 3.4 20.6 - - - +
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Residues in contact with GLY 279 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78A VAL* 3.9 21.5 - - - +
81A PHE* 3.8 18.3 - - - -
82A ALA* 4.2 12.6 - - - -
275A PHE 3.2 17.1 + - - -
278A ALA* 1.3 79.6 - - - +
280A LYS* 1.4 60.3 + - - +
281A ILE 3.5 0.6 + - - -
282A VAL* 3.9 14.7 + - - +
283A GLU* 5.3 1.4 - - - +
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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