Contacts of the helix formed by residues 348 - 362 (chain B) in PDB entry 3E7O
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 ALA 348 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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347B HIS* 1.3 76.3 - - - +
349B ILE* 1.3 61.4 + - + +
350B GLU* 4.3 9.2 - - + +
351B GLU* 2.8 43.1 + - + +
352B TRP* 3.0 10.8 + - - -
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Residues in contact with ILE 349 (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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61B PHE* 4.7 19.9 - - + +
62B GLN 5.4 1.1 - - - +
63B ASN* 3.5 34.8 - - - +
64B GLN* 4.7 7.0 - - + +
67B ALA* 5.7 0.2 - - - -
347B HIS 3.8 0.6 + - - -
348B ALA* 1.3 72.2 - - + +
350B GLU* 1.3 80.9 + - + +
352B TRP* 3.6 11.5 + - + +
353B LYS* 3.1 32.0 + - - +
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Residues in contact with GLU 350 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98B LEU* 5.6 0.9 - - - +
348B ALA* 3.1 6.9 - - + -
349B ILE* 1.3 101.4 - - + +
351B GLU* 1.3 64.7 + - + +
353B LYS* 3.5 27.7 + - - +
354B GLU* 3.3 21.8 + - - +
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Residues in contact with GLU 351 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347B HIS* 3.3 27.4 + - + +
348B ALA* 2.8 34.8 + - + +
350B GLU* 1.3 77.0 - - + +
352B TRP* 1.3 65.3 + - - +
354B GLU* 3.6 6.2 + - - +
355B LEU* 3.2 28.2 + - - +
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Residues in contact with TRP 352 (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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63B ASN 5.1 2.0 - - - -
64B GLN* 4.4 13.1 + - - +
67B ALA* 3.6 31.6 - - + -
68B LYS* 4.1 25.6 - - + -
71B TYR* 3.7 41.1 - + + -
345B ARG* 3.6 46.9 - - + -
346B GLU* 5.0 0.6 + - - +
347B HIS* 3.5 43.0 + + + +
348B ALA 3.0 14.4 + - - -
349B ILE* 3.7 9.6 - - - +
351B GLU* 1.3 75.2 - - - +
353B LYS* 1.3 59.0 + - - +
355B LEU* 3.1 21.1 + - + +
356B ILE* 2.9 34.8 + - + +
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Residues in contact with LYS 353 (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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61B PHE* 3.7 46.1 - - + -
98B LEU* 4.0 19.5 - - + +
99B GLU 5.9 1.6 + - - +
101B PHE* 3.7 32.5 + - + +
349B ILE* 3.1 16.1 + - - +
350B GLU* 3.6 28.3 + - - +
351B GLU 3.3 0.4 - - - -
352B TRP* 1.3 78.6 - - - +
354B GLU* 1.3 56.5 + - - +
356B ILE* 3.5 1.5 + - - +
357B TYR* 2.9 30.0 + - - +
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Residues in contact with GLU 354 (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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98B LEU* 3.4 36.8 - - + +
350B GLU 3.3 13.4 + - - +
351B GLU* 4.1 5.1 - - - +
352B TRP 3.3 0.2 - - - -
353B LYS* 1.3 77.1 - - - +
355B LEU* 1.3 60.4 + - - +
357B TYR* 4.0 2.3 - - + +
358B LYS* 3.1 53.5 + - + +
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Residues in contact with LEU 355 (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 TYR* 3.7 32.7 - - + +
345B ARG* 4.7 13.5 - - - +
347B HIS* 4.1 22.4 - - + +
351B GLU 3.2 17.7 + - - +
352B TRP* 3.1 35.1 + - + +
354B GLU* 1.3 76.8 - - + +
356B ILE* 1.3 65.1 + - - +
358B LYS* 3.5 11.5 + - + +
359B GLU* 3.2 22.0 + - - +
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Residues in contact with ILE 356 (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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57B LEU* 6.1 0.2 - - + -
60B PRO* 4.9 1.6 - - + +
61B PHE* 4.2 21.3 - - + -
67B ALA* 3.8 29.2 - - + +
70B ALA* 4.5 11.2 - - + +
71B TYR* 3.9 29.6 - - + +
74B LEU* 4.4 11.2 - - + -
101B PHE* 3.9 19.3 - - + -
104B VAL* 3.9 17.5 - - + -
352B TRP 2.9 21.8 + - - +
353B LYS 3.9 3.8 - - - +
355B LEU* 1.3 73.6 - - - +
357B TYR* 1.3 64.7 + - - +
359B GLU* 3.1 7.4 + - - +
360B VAL* 3.0 20.4 + - - +
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Residues in contact with TYR 357 (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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93B THR* 4.3 7.9 - - + -
95B GLN 4.5 3.0 + - - -
96B LYS* 3.4 27.2 + - - -
97B THR* 3.5 12.3 - - - -
98B LEU* 3.7 38.4 - - + -
101B PHE* 3.5 38.3 - + + -
353B LYS 2.9 18.8 + - - +
354B GLU* 4.0 4.5 - - + +
355B LEU 3.4 0.2 - - - -
356B ILE* 1.3 75.3 - - - +
358B LYS* 1.3 65.7 + - + +
360B VAL* 3.3 4.2 + - + +
361B MET* 3.2 62.8 + - + +
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Residues in contact with LYS 358 (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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354B GLU* 3.1 48.0 + - + +
355B LEU* 3.6 12.3 - - + +
357B TYR* 1.3 79.4 - - + +
359B GLU* 1.3 63.3 + - - +
361B MET* 3.4 10.0 + - - +
362B ASP* 3.2 18.7 + - - +
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Residues in contact with GLU 359 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B TYR* 3.7 22.6 + - + -
74B LEU* 3.7 28.0 - - + -
75B VAL* 3.8 22.6 - - + +
78B LYS* 3.0 41.3 + - + +
91B VAL* 4.6 4.7 - - - +
355B LEU 3.2 8.8 + - - +
356B ILE* 3.1 11.7 + - - +
358B LYS* 1.3 81.1 - - - +
360B VAL* 1.3 59.5 + - - +
362B ASP* 2.8 19.0 - - - +
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Residues in contact with VAL 360 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74B LEU* 3.8 16.8 - - + -
91B VAL* 4.0 24.3 - - + +
92B PHE* 3.7 32.7 - - - -
93B THR* 3.7 20.2 - - + +
101B PHE* 4.7 3.8 - - + -
104B VAL* 3.9 28.0 - - + -
356B ILE 3.0 14.4 + - - +
357B TYR* 3.3 10.0 + - + +
359B GLU* 1.3 76.6 - - - +
361B MET* 1.3 62.5 + - - +
362B ASP 3.8 4.7 + - - +
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Residues in contact with MET 361 (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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93B THR* 4.1 17.7 - - - -
95B GLN 5.3 2.5 - - - +
96B LYS* 6.5 0.4 - - - -
357B TYR* 3.2 57.4 + - + +
358B LYS* 3.4 6.0 + - - +
359B GLU 3.3 0.8 - - - -
360B VAL* 1.3 80.0 - - - +
362B ASP* 1.3 65.5 + - - +
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Residues in contact with ASP 362 (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 LYS* 2.7 36.4 + - - -
91B VAL* 5.7 2.9 - - - +
358B LYS 3.2 12.5 + - - +
359B GLU* 2.8 17.0 - - - +
360B VAL 4.1 5.9 - - - +
361B MET* 1.3 83.6 - - - +
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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