Contacts of the helix formed by residues 437 - 445 (chain A) in PDB entry 2QTL
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 PRO 437 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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248A GLU* 4.5 2.2 - - - +
391A TYR* 3.6 42.0 - - + +
435A GLN 3.9 0.4 - - - +
436A PRO* 1.3 89.7 - - + +
438A LEU* 1.3 66.0 + - - +
439A SER* 3.8 16.4 - - - +
440A LEU* 3.0 29.3 + - + +
441A LEU* 3.5 7.3 + - - +
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Residues in contact with LEU 438 (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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252A VAL* 3.7 26.7 - - + -
254A LEU* 4.1 13.5 - - + -
331A LEU* 5.9 1.7 - - - +
333A LEU* 4.1 25.5 - - + +
341A VAL* 4.9 1.6 - - + -
366A LEU* 3.7 21.3 - - + -
370A PHE* 3.7 37.2 - - + -
436A PRO 3.9 1.4 + - - -
437A PRO* 1.3 70.5 - - - +
439A SER* 1.3 64.7 + - - +
440A LEU 3.1 0.5 + - - -
441A LEU* 3.1 14.2 + - + +
442A LEU* 3.1 37.4 + - + +
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Residues in contact with SER 439 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248A GLU* 4.7 2.8 + - - -
250A LEU* 3.4 29.3 + - - +
252A VAL* 3.8 27.1 - - - +
346A LYS* 4.2 10.8 + - - -
437A PRO* 3.8 16.1 - - - +
438A LEU* 1.3 78.4 - - - +
440A LEU* 1.3 62.8 + - - +
442A LEU* 3.3 4.4 + - - +
443A GLU* 3.1 28.9 + - - +
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Residues in contact with LEU 440 (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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246A PRO* 6.3 0.2 - - + -
248A GLU* 4.0 16.8 - - + +
384A PHE* 4.1 7.1 - - + -
387A ALA* 3.5 32.1 - - + +
388A LEU* 4.0 12.6 - - + -
391A TYR* 3.9 28.5 - - + -
436A PRO* 4.0 15.7 - - + -
437A PRO* 3.0 19.3 + - + +
439A SER* 1.3 79.5 + - - +
441A LEU* 1.3 65.3 + - - +
443A GLU* 3.2 19.2 + - - +
444A HIS* 3.2 41.5 + - + +
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Residues in contact with LEU 441 (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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327A LEU* 4.9 0.4 - - + -
331A LEU* 3.2 37.7 - - + -
370A PHE* 4.1 16.4 - - + -
384A PHE* 4.3 13.2 - - + -
424A LEU* 3.6 31.6 - - + -
436A PRO* 3.7 29.4 - - + -
437A PRO 3.7 13.0 - - - +
438A LEU* 3.1 16.4 + - + +
440A LEU* 1.3 76.6 - - - +
442A LEU* 1.3 60.3 + - + +
444A HIS 3.0 1.7 + - - -
445A LEU* 2.8 41.2 + - + +
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Residues in contact with LEU 442 (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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249A TYR* 5.0 0.2 + - - -
250A LEU* 3.6 20.8 - - + +
252A VAL* 4.0 10.5 - - + -
341A VAL* 4.1 15.0 - - + -
343A LEU* 4.0 25.8 - - + -
357A PRO* 3.9 8.3 - - - +
359A HIS* 5.1 1.2 + - - -
360A ILE* 3.7 33.4 - - + +
366A LEU* 6.1 0.9 - - + -
369A ILE* 4.6 5.4 - - + -
370A PHE* 4.5 4.0 - - + -
374A LEU* 3.7 30.1 - - + -
438A LEU* 3.1 34.0 + - + +
439A SER* 3.3 3.6 + - - +
440A LEU 3.2 0.4 - - - -
441A LEU* 1.3 77.4 - - - +
443A GLU* 1.3 57.4 + - - +
444A HIS 3.4 0.2 - - - -
445A LEU* 4.6 6.5 - - - +
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Residues in contact with GLU 443 (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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246A PRO* 6.1 0.5 - - - +
247A PRO 4.7 1.0 - - - +
248A GLU* 3.4 17.5 - - - +
249A TYR* 2.7 66.8 + - + -
250A LEU* 2.9 22.9 + - + +
346A LYS* 4.5 0.9 + - - -
439A SER* 3.1 17.7 + - - +
440A LEU* 3.5 27.2 - - - +
442A LEU* 1.3 77.9 - - - +
444A HIS* 1.3 72.8 + - + +
445A LEU 5.3 0.2 - - - -
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Residues in contact with HIS 444 (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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246A PRO* 4.2 28.3 - - + +
383A ALA* 4.3 4.4 - - + +
384A PHE* 3.6 53.4 + + + +
387A ALA* 4.3 5.9 - - - +
440A LEU* 3.2 45.2 + - + +
441A LEU 3.0 2.8 + - - -
443A GLU* 1.3 92.9 + - + +
445A LEU* 1.3 66.9 + - - +
446A PRO* 3.4 8.1 - - - +
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Residues in contact with LEU 445 (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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327A LEU* 5.1 1.3 - - + -
359A HIS* 3.3 16.1 + - - -
370A PHE* 4.4 7.0 - - + -
374A LEU* 4.1 36.3 - - + +
375A GLU 3.9 17.7 - - - +
376A ILE* 4.3 19.3 - - + +
378A ALA* 5.0 5.2 - - + +
384A PHE* 4.4 15.9 - - + -
424A LEU* 4.3 15.3 - - + -
441A LEU* 2.8 47.1 + - + +
442A LEU 4.7 4.3 - - - +
443A GLU 5.3 0.3 - - - -
444A HIS* 1.3 72.0 - - - +
446A PRO* 1.4 71.4 - - + +
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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