Contacts of the helix formed by residues 374 - 389 (chain A) in PDB entry 1K89
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 ALA 374 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113A LYS* 4.1 12.3 - - + +
116A LEU* 5.5 1.1 - - + -
117A THR* 4.4 6.2 - - + +
370A LYS 4.0 10.2 + - - +
371A ALA* 3.3 16.0 + - - +
372A VAL 3.2 4.0 + - - -
373A ASN* 1.3 76.8 + - - +
375A GLY* 1.3 56.4 + - - +
376A GLY 3.2 0.9 - - - -
377A VAL* 3.2 14.9 + - + +
378A LEU* 2.9 27.9 + - - +
406A MET* 4.2 2.7 - - + -
409A ILE* 3.8 24.0 - - + -
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Residues in contact with GLY 375 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208A ALA 3.9 15.5 - - - -
209A THR* 4.8 1.3 + - - +
212A GLY* 4.6 2.9 - - - -
372A VAL 4.6 0.8 + - - -
373A ASN 2.9 3.8 + - - -
374A ALA* 1.3 73.9 - - - +
376A GLY* 1.3 66.2 + - - +
378A LEU* 3.5 1.7 - - - +
379A VAL* 3.0 29.8 + - - +
402A LEU* 3.8 23.3 - - - -
406A MET* 3.8 11.6 - - - +
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Residues in contact with GLY 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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205A ARG 5.9 0.2 - - - -
208A ALA* 4.1 8.0 - - - +
209A THR* 3.5 23.9 + - - +
373A ASN 3.5 7.3 + - - -
374A ALA 3.2 0.6 - - - -
375A GLY* 1.3 79.8 - - - +
377A VAL* 1.3 61.1 + - - +
379A VAL* 3.3 2.6 + - - +
380A SER* 3.1 22.3 + - - -
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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
----------------------------------------------------------
89A LEU* 4.2 10.1 - - + -
110A GLN* 3.3 28.3 - - - +
113A LYS* 3.9 24.2 - - + +
114A ASP* 3.6 15.5 - - - +
117A THR* 3.8 15.5 - - + -
121A MET* 3.8 14.6 - - + +
373A ASN 4.5 1.4 + - - -
374A ALA* 3.3 15.9 - - - +
376A GLY* 1.3 75.4 - - - +
378A LEU* 1.3 57.1 + - - +
380A SER* 3.1 10.1 + - - +
381A GLY 2.9 24.3 + - - -
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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
----------------------------------------------------------
117A THR* 3.6 31.6 - - + +
119A LEU* 3.7 25.4 - - + +
374A ALA 2.9 14.8 + - - +
375A GLY* 3.5 5.8 - - - +
376A GLY 3.1 0.2 - - - -
377A VAL* 1.3 77.8 - - - +
379A VAL* 1.3 57.1 + - - +
381A GLY* 3.1 4.3 + - - -
382A PHE* 3.0 50.5 + - + -
402A LEU* 4.0 12.3 - - + +
405A VAL* 3.2 34.3 - - + -
406A MET* 3.9 23.8 - - - -
409A ILE* 4.8 2.9 - - + -
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Residues in contact with VAL 379 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202A SER* 3.9 19.5 - - - +
203A LEU 4.1 4.3 - - - +
204A VAL 4.3 1.8 - - - +
205A ARG* 3.9 29.4 - - + +
208A ALA* 3.3 29.8 - - + -
375A GLY 3.0 7.8 + - - +
376A GLY 4.0 1.8 - - - +
378A LEU* 1.3 71.2 - - - +
380A SER* 1.3 59.6 + - - +
382A PHE* 3.2 11.5 + - + +
383A GLU* 2.8 29.5 + - - +
398A VAL* 4.1 20.0 - - + -
402A LEU* 4.6 11.2 - - + -
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Residues in contact with SER 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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89A LEU* 4.7 15.0 - - - -
163A ALA* 4.4 6.9 - - - +
193A THR* 3.0 32.3 + - - +
194A GLY 5.0 1.4 + - - -
376A GLY 3.1 14.6 + - - -
377A VAL* 3.1 15.0 + - - +
379A VAL* 1.3 77.2 - - - +
381A GLY* 1.3 61.7 + - - +
383A GLU* 3.2 6.6 + - - +
384A MET* 3.0 28.3 + - - +
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Residues in contact with GLY 381 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119A LEU* 3.9 16.6 - - - -
121A MET* 4.1 12.9 - - - -
377A VAL 2.9 12.6 + - - -
378A LEU 3.1 4.4 + - - -
380A SER* 1.3 78.1 - - - +
382A PHE* 1.3 58.7 + - - +
384A MET* 3.3 12.8 + - - +
385A SER* 2.9 30.2 + - - -
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Residues in contact with PHE 382 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119A LEU* 4.0 25.6 - - + -
202A SER* 4.8 2.7 - - - +
378A LEU* 3.0 36.6 + - + -
379A VAL* 3.2 13.0 + - + +
381A GLY* 1.3 77.0 - - - +
383A GLU* 1.3 59.1 + - - +
385A SER* 3.2 4.1 + - - -
386A GLN* 2.9 40.4 + - - +
393A TRP* 3.6 29.8 - + + -
398A VAL* 3.8 29.2 - - + -
401A LYS* 3.5 41.5 - - + -
402A LEU* 3.9 11.7 - - + -
405A VAL* 5.0 4.3 - - + -
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Residues in contact with GLU 383 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193A THR* 3.3 7.9 - - + -
194A GLY* 3.1 23.4 + - - -
195A LYS* 2.6 46.5 + - - +
200A GLY 3.6 17.0 - - - +
201A GLY* 3.9 12.3 - - - -
202A SER* 3.8 15.7 + - - +
205A ARG* 4.8 7.4 - - - +
379A VAL 2.8 14.3 + - - +
380A SER* 3.2 10.6 + - - +
382A PHE* 1.3 74.5 - - - +
384A MET* 1.3 56.8 + - - +
386A GLN* 3.1 12.2 + - + +
387A ASN* 2.8 34.4 + - - -
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Residues in contact with MET 384 (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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87A PRO* 4.1 22.7 - - + -
89A LEU* 3.5 31.2 - - + -
120A PRO 5.4 4.3 - - - +
121A MET* 5.3 3.1 - - + -
157A PRO 4.4 5.8 - - - +
161A VAL* 4.0 25.8 - - + -
190A GLY* 4.5 9.1 - - - +
193A THR* 3.6 14.4 - - + -
380A SER 3.0 18.7 + - - +
381A GLY* 3.5 12.1 - - - +
383A GLU* 1.3 76.1 - - - +
385A SER* 1.3 57.2 + - - +
387A ASN* 3.3 9.0 + - - +
388A SER* 2.9 33.1 + - - -
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Residues in contact with SER 385 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119A LEU* 6.1 0.9 - - - +
381A GLY 2.9 15.6 + - - -
382A PHE* 3.5 9.0 - - - -
384A MET* 1.3 77.8 - - - +
386A GLN* 1.3 56.6 + - - +
388A SER* 3.2 6.5 + - - -
389A GLU* 2.9 37.3 + - - +
393A TRP* 3.7 25.1 - - - -
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Residues in contact with GLN 386 (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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197A ARG* 4.7 1.2 + - - -
200A GLY 5.6 1.6 - - - +
201A GLY 5.3 0.2 - - - +
202A SER* 3.0 38.6 + - - -
203A LEU 5.1 0.2 + - - -
382A PHE* 2.9 28.0 + - - +
383A GLU* 3.6 4.3 - - - +
385A SER* 1.3 75.2 - - - +
387A ASN* 1.3 63.8 + - - +
389A GLU* 3.3 6.1 + - - +
390A ARG 2.9 24.3 + - - -
391A LEU 3.1 23.5 + - - +
392A SER* 3.4 7.6 + - - -
393A TRP* 2.7 65.6 + - + +
398A VAL* 4.2 2.5 - - - +
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Residues in contact with ASN 387 (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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189A ASN* 3.6 29.9 - - - +
190A GLY* 3.4 21.2 - - - -
195A LYS* 2.6 27.9 + - - -
200A GLY* 2.9 28.3 + - - -
383A GLU* 2.8 22.1 + - - +
384A MET* 3.8 4.2 - - - +
386A GLN* 1.3 81.9 - - - +
388A SER* 1.3 61.3 + - - +
390A ARG* 3.3 19.4 + - - +
391A LEU 5.5 0.4 + - - -
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Residues in contact with SER 388 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384A MET* 2.9 20.0 + - - +
385A SER* 3.2 7.6 + - - -
387A ASN* 1.3 77.0 - - - +
389A GLU* 1.3 62.2 + - - +
390A ARG* 3.5 11.6 + - - +
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Residues in contact with GLU 389 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385A SER* 2.9 22.4 + - - +
386A GLN* 3.9 0.8 - - - +
388A SER* 1.3 77.0 - - - +
390A ARG* 1.3 71.1 + - - +
391A LEU* 3.0 43.3 - - + +
393A TRP* 3.0 24.5 + - - -
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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
------------------------------------------------------------
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