Contacts of the helix formed by residues 373 - 380 (chain A) in PDB entry 4KTQ
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 373 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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306A PHE* 5.0 1.8 - - + -
350A GLY* 3.8 14.6 - - - -
351A LEU* 3.4 29.2 - - + +
371A ASP 4.8 0.2 - - - -
372A ASP* 1.3 83.9 - - - +
374A MET* 1.3 57.9 + - - +
376A LEU* 2.4 49.4 + - + +
377A ALA* 3.2 4.3 + - - -
390A VAL* 5.6 1.1 - - + -
409A SER* 4.2 11.0 - - - +
412A LEU* 4.0 21.8 - - + -
413A PHE* 4.1 19.7 - - + +
416A LEU* 4.4 9.9 - - + -
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Residues in contact with MET 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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351A LEU* 3.2 28.8 - - + +
352A LEU* 4.4 15.0 - - + +
372A ASP* 3.1 16.8 + - - +
373A PRO* 1.3 79.0 - - - +
375A LEU* 1.3 61.8 + - - +
377A ALA* 3.4 6.4 + - - +
378A TYR* 3.1 23.4 + - - +
384A ASN 4.6 0.9 - - - +
385A THR* 3.4 27.8 - - - +
386A THR* 3.5 13.0 - - - +
387A PRO* 3.8 2.2 - - + -
390A VAL* 3.4 28.4 - - + +
567A THR* 2.8 39.5 - - + +
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Residues in contact with LEU 375 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372A ASP* 3.2 23.7 + - + +
373A PRO 2.7 4.2 + - - -
374A MET* 1.3 76.8 - - - +
376A LEU* 1.3 60.6 - - - +
378A TYR* 3.5 5.1 + - + +
379A LEU* 3.2 27.1 + - - +
430A TYR* 3.3 19.5 - - + -
434A GLU* 3.3 22.2 - - + +
435A ARG* 3.2 36.6 - - + +
438A SER* 5.2 3.8 - - - -
566A GLN* 3.0 36.3 - - - +
567A THR* 4.1 17.0 - - + +
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Residues in contact with LEU 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 ASP 3.8 1.8 - - - +
373A PRO* 2.4 26.4 + - + +
375A LEU* 1.3 66.3 - - - +
377A ALA* 1.3 64.7 + - - +
379A LEU* 3.1 8.7 + - - +
380A LEU* 3.0 26.2 + - + +
413A PHE* 3.8 30.5 - - + -
416A LEU* 3.8 28.9 - - + -
417A TRP* 3.9 14.1 - - + +
420A LEU* 3.6 26.2 - - + +
430A TYR* 3.3 46.7 - - + -
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Residues in contact with ALA 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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373A PRO 3.2 5.6 + - - +
374A MET 3.8 7.2 - - - +
376A LEU* 1.3 77.2 - - - +
378A TYR* 1.3 56.0 - - - +
380A LEU* 2.9 6.8 + - - -
381A ASP 2.6 36.7 + - - +
384A ASN* 3.4 29.4 + - + +
390A VAL* 4.0 21.5 - - + -
394A TYR* 4.5 5.8 - - + -
416A LEU* 4.3 12.4 - - + +
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Residues in contact with TYR 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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374A MET 3.1 5.5 + - - +
375A LEU* 3.6 5.4 - - + +
377A ALA* 1.3 79.3 - - - +
379A LEU* 1.3 61.9 + - + +
381A ASP 3.6 5.6 - - - -
382A PRO* 3.2 38.1 - - + +
384A ASN* 3.4 14.9 - - - +
434A GLU* 5.1 5.2 - - - -
566A GLN 3.6 15.5 - - - -
567A THR* 3.3 52.0 - - + -
568A ALA 3.7 0.2 - - - -
569A THR* 2.5 39.6 + - - -
572A GLY* 3.0 24.2 - - - -
573A ARG 3.8 1.2 + - - -
726A ARG* 3.9 26.4 + - - +
762A LYS* 4.7 4.3 - - - -
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Residues in contact with LEU 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 LEU 3.2 16.1 + - - +
376A LEU* 3.1 8.9 + - + +
377A ALA 3.0 0.8 - - - -
378A TYR* 1.3 83.4 - - + +
380A LEU* 1.3 64.8 + - + +
382A PRO* 4.4 5.0 - - - +
420A LEU* 6.0 4.0 - - + -
426A LEU* 3.3 40.5 - - + +
429A LEU* 4.7 7.9 - - + -
430A TYR* 3.4 45.5 - - + +
434A GLU* 3.8 17.9 - - + -
726A ARG* 3.6 32.1 - - + +
727A ARG* 4.7 8.0 + - - +
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Residues in contact with LEU 380 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376A LEU* 3.0 14.0 + - + +
377A ALA* 2.9 7.3 + - - +
379A LEU* 1.3 77.8 - - - +
381A ASP* 1.3 63.4 + - + +
382A PRO* 4.3 2.3 - - - +
394A TYR* 4.8 8.7 - - + +
416A LEU* 3.3 35.9 - - + +
419A ARG* 4.0 30.5 - - + +
420A LEU* 3.7 28.9 - - + -
423A GLU* 4.9 4.9 - - + -
426A LEU* 3.9 13.0 - - + -
727A ARG* 4.7 6.6 - - - +
729A TYR* 4.1 15.9 - - - -
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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