Contacts of the helix formed by residues 407 - 419 (chain A) in PDB entry 2W2Q
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 THR 407 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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310A VAL* 6.1 0.2 - - - -
400A LEU* 6.2 0.2 - - - -
405A GLU 4.5 5.4 - - - +
406A LEU* 1.3 78.3 - - - +
408A LEU* 1.3 64.8 + - - +
409A ALA* 4.0 6.6 + - - +
410A GLU* 3.2 39.2 + - - +
411A LEU* 3.1 23.4 + - - +
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Residues in contact with LEU 408 (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 ALA* 3.7 36.6 - - + +
308A GLY* 4.8 14.9 + - - +
309A VAL 3.9 11.0 - - - +
310A VAL* 3.9 33.0 - - + -
311A LEU 5.2 1.3 - - - +
332A GLU* 4.3 22.9 - - - +
334A ILE* 4.8 12.1 - - + -
407A THR* 1.3 73.6 - - - +
409A ALA* 1.3 62.3 + - - +
411A LEU* 3.5 4.6 + - + +
412A ARG* 3.1 34.4 + - - +
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Residues in contact with ALA 409 (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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407A THR* 3.3 7.9 + - - +
408A LEU* 1.3 79.2 - - - +
410A GLU* 1.3 63.2 + - + +
412A ARG* 3.7 5.9 + - - +
413A GLN* 3.2 28.4 + - - +
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Residues in contact with GLU 410 (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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405A GLU 4.4 1.9 - - - +
406A LEU* 3.7 25.1 - - + +
407A THR* 3.2 38.7 + - - +
408A LEU 3.3 0.6 - - - -
409A ALA* 1.3 78.1 - - + +
411A LEU* 1.3 59.5 + - - +
413A GLN* 3.5 5.0 + - - +
414A ARG* 2.9 38.5 + - - +
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Residues in contact with LEU 411 (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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310A VAL* 3.7 41.5 - - + -
334A ILE* 4.5 3.1 - - + -
396A ALA* 4.0 14.8 - - + +
399A MET* 3.8 35.9 - - + -
400A LEU* 3.8 23.6 - - + -
406A LEU* 4.0 11.1 - - + +
407A THR 3.1 16.2 + - - +
408A LEU* 3.8 5.2 - - + +
410A GLU* 1.3 73.3 - - - +
412A ARG* 1.3 61.1 + - - +
414A ARG* 3.2 7.1 + - - +
415A LEU* 2.8 41.3 + - + +
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Residues in contact with ARG 412 (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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331A PRO* 3.0 25.7 + - - +
332A GLU* 3.4 26.9 + - - +
333A VAL 2.8 30.2 + - - -
334A ILE* 3.8 22.3 - - + +
360A ASP* 3.0 29.8 + - + -
408A LEU* 3.1 26.5 + - - +
409A ALA* 3.8 6.5 - - - +
411A LEU* 1.3 78.0 - - - +
413A GLN* 1.3 60.8 + - - +
415A LEU* 3.3 12.7 + - + +
416A ILE* 3.1 39.5 + - + +
1448A CA 3.9 1.0 - - - -
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Residues in contact with GLN 413 (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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409A ALA 3.2 17.2 + - - +
410A GLU* 3.5 5.4 + - - +
412A ARG* 1.3 78.8 - - + +
414A ARG* 1.3 60.1 + - - +
416A ILE* 3.6 31.9 - - - +
417A HIS* 3.0 31.3 + - - +
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Residues in contact with ARG 414 (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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399A MET* 4.1 20.3 - - + +
403A GLU* 2.5 37.4 + - - -
406A LEU* 3.8 25.4 - - + +
410A GLU* 2.9 22.2 + - - +
411A LEU* 3.3 13.0 - - - +
413A GLN* 1.3 75.0 - - - +
415A LEU* 1.3 57.6 + - - +
417A HIS* 3.5 4.7 + - - -
418A PHE* 3.1 57.8 + - + +
445A PRO* 6.3 0.2 - - + -
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Residues in contact with LEU 415 (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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334A ILE* 3.9 32.3 - - + -
361A LEU* 4.6 16.2 - - + -
392A VAL* 4.4 21.3 - - + +
395A ILE* 3.7 30.1 - - + -
396A ALA* 5.3 3.8 - - + +
399A MET* 4.3 10.3 - - + -
411A LEU* 2.8 27.8 + - + +
412A ARG* 3.4 11.4 - - + +
414A ARG* 1.3 73.8 - - - +
416A ILE* 1.3 60.2 + - + +
418A PHE* 3.5 1.3 + - - -
419A SER* 2.6 34.6 + - - -
442A ALA* 5.2 4.7 - - + -
443A ALA 5.1 5.0 + - - +
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Residues in contact with ILE 416 (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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360A ASP* 5.2 6.3 - - + +
361A LEU* 5.8 2.5 - - + -
412A ARG* 3.1 21.3 + - + +
413A GLN* 3.6 34.3 - - - +
415A LEU* 1.3 73.8 - - + +
417A HIS* 1.3 60.0 + - - +
418A PHE 3.4 0.3 + - - -
419A SER* 3.4 13.4 + - - -
421A LYS* 2.9 26.9 + - - -
440A LEU* 4.1 30.4 - - + +
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Residues in contact with HIS 417 (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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413A GLN* 3.0 20.0 + - - +
414A ARG* 3.7 6.3 - - - +
416A ILE* 1.3 78.4 - - - +
418A PHE* 1.3 92.2 + + - +
419A SER 3.9 0.3 - - - +
421A LYS* 2.8 21.5 + - - +
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Residues in contact with PHE 418 (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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399A MET* 4.6 4.3 - - + -
414A ARG* 3.1 51.5 + - + +
415A LEU 4.0 1.3 - - - +
417A HIS* 1.3 100.2 - + - +
419A SER* 1.3 64.3 + - - +
443A ALA* 3.4 33.3 - - - +
444A LEU 4.5 5.8 - - - +
445A PRO* 4.2 19.5 - - + -
446A PRO* 3.7 32.5 - - + -
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Residues in contact with SER 419 (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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361A LEU* 3.8 10.7 - - - +
415A LEU 2.6 22.6 + - - -
416A ILE* 3.5 10.6 - - - -
417A HIS 3.3 0.9 - - - +
418A PHE* 1.3 80.8 - - - +
420A ALA* 1.3 61.3 + - - +
421A LYS* 3.0 21.8 + - - +
440A LEU* 4.0 20.0 - - - +
441A VAL 3.3 14.6 - - - -
442A ALA* 3.7 13.9 - - - -
443A ALA 4.2 2.9 - - - +
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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