Contacts of the helix formed by residues 373 - 380 (chain A) in PDB entry 3E5A
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 MET 373 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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308A GLU* 4.9 11.2 - - - +
309A LYS* 4.4 21.1 - - - -
312A LEU* 4.6 1.8 - - - -
372A PRO* 1.3 77.6 - - - +
374A LEU* 1.3 61.3 + - - +
375A ARG* 3.2 28.5 - - + +
376A GLU* 3.0 33.9 + - + +
377A VAL* 3.2 5.9 + - - +
600A SO4 3.2 33.2 - - - +
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Residues in contact with LEU 374 (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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241A ALA* 4.2 18.1 - - + +
244A LEU* 3.6 16.8 - - + -
245A SER* 3.3 38.4 - - - +
248A HIS* 3.6 22.4 - - + +
312A LEU* 3.8 28.7 - - + +
315A LEU* 3.9 20.2 - - + -
372A PRO 4.1 0.2 + - - -
373A MET* 1.3 70.5 - - - +
375A ARG* 1.3 57.0 + - - +
377A VAL* 3.3 7.4 + - + +
378A LEU* 3.0 33.7 + - + +
600A SO4 2.8 25.0 + - - +
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Residues in contact with ARG 375 (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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245A SER* 5.3 0.6 + - - +
373A MET* 3.9 18.6 - - + +
374A LEU* 1.3 76.2 - - - +
376A GLU* 1.3 65.1 + - + +
378A LEU* 3.4 12.6 + - + +
379A GLU* 3.0 44.8 + - - +
600A SO4 3.0 37.1 + - - +
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Residues in contact with GLU 376 (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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372A PRO* 3.2 31.5 - - + +
373A MET* 3.0 29.2 + - + +
375A ARG* 1.3 80.3 - - + +
377A VAL* 1.3 64.5 + - - +
378A LEU 3.2 0.2 - - - -
379A GLU* 3.1 6.8 + - - -
380A HIS* 2.8 24.5 + - - +
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Residues in contact with VAL 377 (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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237A ILE* 4.0 27.1 - - + -
238A THR* 6.2 0.2 - - - -
241A ALA* 4.3 13.5 - - + -
312A LEU* 4.4 7.9 - - + -
315A LEU* 4.5 6.7 - - + -
359A LEU* 4.4 15.5 - - + -
363A LEU* 3.9 27.8 - - + -
372A PRO* 4.3 8.3 - - + +
373A MET 3.2 10.2 + - - +
374A LEU* 3.3 9.8 + - - +
376A GLU* 1.3 76.9 - - - +
378A LEU* 1.3 64.6 + - - +
380A HIS* 2.9 22.6 + - - +
383A ILE* 3.6 12.1 - - + +
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Residues in contact with LEU 378 (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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238A THR* 3.6 37.2 + - + +
241A ALA* 3.9 15.3 - - + -
242A ASN* 3.4 33.4 - - - +
245A SER* 4.9 8.3 - - - +
374A LEU 3.0 21.7 + - - +
375A ARG* 3.6 15.7 - - + +
376A GLU 3.2 0.2 - - - -
377A VAL* 1.3 76.1 - - - +
379A GLU* 1.3 63.2 + - + +
383A ILE* 3.9 11.6 - - - +
384A THR* 3.7 14.0 - - - +
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Residues in contact with GLU 379 (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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375A ARG* 3.0 32.4 + - - +
376A GLU* 3.1 6.5 + - - +
377A VAL 3.1 0.6 - - - -
378A LEU* 1.3 81.4 - - + +
380A HIS* 1.3 63.3 + - - +
381A PRO* 3.4 5.5 - - - +
384A THR* 3.9 11.8 - - + +
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Residues in contact with HIS 380 (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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355A GLY* 3.4 27.1 - - - -
358A ASP* 3.1 27.1 + - + -
359A LEU* 3.8 28.8 + - + +
362A ARG* 4.4 11.2 - - - -
376A GLU 2.8 11.9 + - - +
377A VAL 2.9 15.7 + - - +
379A GLU* 1.3 75.8 - - - +
381A PRO* 1.4 66.7 - - + +
382A TRP* 3.2 31.7 + - + +
383A ILE* 2.8 30.0 + - + +
384A THR* 2.9 16.1 + - - -
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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