Contacts of the helix formed by residues 340 - 349 (chain A) in PDB entry 5E2Q
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 340 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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335A VAL* 3.8 2.8 - - - +
336A ASN 2.6 23.3 + - - -
337A LYS* 3.9 8.7 - - - -
338A ALA 3.2 0.8 - - - -
339A MET* 1.3 76.1 - - - +
341A ALA* 1.3 62.0 + - - +
342A LYS 3.5 0.4 - - - -
343A PHE* 3.7 6.0 + - - +
344A GLU* 3.2 38.5 + - - +
374A THR* 3.5 15.1 - - - +
375A SER 2.6 34.1 + - - +
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Residues in contact with ALA 341 (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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337A LYS 3.6 6.1 + - - +
338A ALA* 3.4 16.1 + - - +
339A MET 3.1 0.6 - - - -
340A SER* 1.3 79.7 - - - +
342A LYS* 1.3 63.0 + - - +
343A PHE 3.4 0.2 + - - -
344A GLU* 3.5 10.9 + - - +
345A ARG* 3.2 34.4 + - - +
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Residues in contact with LYS 342 (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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338A ALA 5.8 0.2 - - - +
339A MET* 3.6 27.2 - - - +
341A ALA* 1.3 78.4 - - - +
343A PHE* 1.3 83.2 + - + +
344A GLU 3.4 0.2 - - - -
345A ARG* 3.3 18.4 - - - +
346A LEU* 3.0 21.7 + - - +
444A ASP* 2.5 30.2 + - - -
527A ILE* 3.2 30.8 - - + +
528A PHE* 3.6 28.3 + - + +
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Residues in contact with PHE 343 (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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339A MET* 3.1 30.1 - - + -
340A SER* 4.0 8.3 - - - +
341A ALA 3.2 1.0 - - - -
342A LYS* 1.3 87.8 - - + +
344A GLU* 1.3 59.7 + - - +
345A ARG 3.1 1.6 - - - -
346A LEU* 3.1 8.0 + - + +
347A VAL* 3.0 31.6 + - - +
373A PHE* 3.5 54.6 - + + +
374A THR 4.7 0.4 - - - -
375A SER* 3.8 20.2 - - - -
408A SER* 3.7 17.0 - - - -
413A LEU* 5.8 0.2 - - + -
444A ASP* 3.7 27.1 - - - -
447A VAL* 5.6 0.2 - - + -
448A GLY* 4.4 3.6 - - - -
528A PHE* 3.8 24.0 - + - -
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Residues in contact with GLU 344 (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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305A GLY* 6.2 0.2 - - - -
337A LYS* 5.5 1.9 + - - +
340A SER* 3.2 32.0 + - - +
341A ALA* 3.9 7.6 - - - +
343A PHE* 1.3 75.1 - - - +
345A ARG* 1.3 59.3 + - - +
347A VAL* 3.4 11.2 + - - +
348A ALA* 3.0 26.5 + - - +
372A ASP* 5.2 4.1 - - - +
373A PHE 3.5 16.0 - - - +
374A THR* 4.4 7.6 - - - +
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Residues in contact with ARG 345 (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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341A ALA* 3.2 20.9 + - - +
342A LYS* 3.3 34.6 - - - +
344A GLU* 1.3 77.8 - - - +
346A LEU* 1.3 61.7 + - - +
348A ALA* 3.4 15.9 + - + +
349A SER* 3.5 9.4 + - - -
526A GLU 4.5 2.8 + - - -
527A ILE* 2.6 60.0 + - + +
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Residues in contact with LEU 346 (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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342A LYS 3.0 14.5 + - - +
343A PHE* 3.4 10.5 - - + +
345A ARG* 1.3 75.4 - - - +
347A VAL* 1.3 58.3 + - - +
349A SER* 3.5 1.9 + - - -
350A ALA* 3.0 27.4 + - - +
353A LEU* 3.8 24.2 - - + -
373A PHE* 4.6 3.8 - - + -
448A GLY* 4.0 22.2 - - - +
449A LEU* 4.0 23.3 - - + -
452A LEU* 3.7 18.4 - - + -
453A LEU* 4.2 1.3 - - + -
524A VAL* 4.5 9.6 - - + -
527A ILE* 3.7 19.0 - - + +
528A PHE* 4.1 19.1 - - + -
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Residues in contact with VAL 347 (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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343A PHE 3.0 19.3 + - - +
344A GLU* 3.6 10.5 - - - +
345A ARG 3.3 0.2 - - - -
346A LEU* 1.3 76.5 - - - +
348A ALA* 1.3 63.9 + - - +
349A SER 3.1 0.4 - - - -
350A ALA* 3.1 20.4 + - - +
368A PHE* 3.6 13.6 - - + -
370A THR* 4.3 13.2 - - + -
371A PRO* 3.5 38.8 - - + +
373A PHE* 3.6 24.7 - - + +
452A LEU* 3.8 15.7 - - + -
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Residues in contact with ALA 348 (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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344A GLU 3.0 16.9 + - - +
345A ARG* 3.5 11.4 - - + +
346A LEU 3.3 0.4 - - - -
347A VAL* 1.3 77.7 - - - +
349A SER* 1.3 57.8 + - - +
351A GLU* 5.3 2.4 + - - +
368A PHE* 6.1 0.2 - - - -
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Residues in contact with SER 349 (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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345A ARG 3.5 3.7 + - - -
346A LEU 3.5 4.9 + - - -
347A VAL 3.1 0.4 - - - -
348A ALA* 1.3 77.4 - - - +
350A ALA* 1.3 63.7 + - - +
351A GLU* 3.3 2.2 - - - -
352A GLN* 3.6 12.1 + - - +
353A LEU* 3.2 25.4 + - - +
523A GLN* 3.6 23.7 + - - -
527A ILE* 3.6 24.3 - - - +
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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