Contacts of the helix formed by residues 342 - 359 (chain A) in PDB entry 1KAS
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 LEU 342 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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107A GLY* 5.3 1.6 - - - -
108A ILE* 3.7 29.2 - - + -
162A ALA* 3.9 10.5 - - + +
163A CYS* 3.7 20.8 - - - +
191A GLU* 3.4 11.9 - - + +
193A ALA* 4.1 9.0 - - + -
202A PHE* 3.7 28.7 - - + -
229A PHE* 5.1 1.3 - - + -
231A LEU* 3.8 22.0 - - + -
340A HIS* 3.2 30.5 + - + +
341A LEU* 1.3 74.7 - - - +
343A GLY* 1.3 60.8 + - - +
345A ALA* 3.1 22.2 + - - +
346A GLY 4.5 0.2 + - - -
400A PHE* 4.1 14.6 - - + -
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Residues in contact with GLY 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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105A GLY 4.6 0.2 - - - +
106A SER* 4.4 0.9 - - - -
107A GLY 3.7 5.6 - - - +
162A ALA 3.5 15.6 + - - -
165A SER* 3.5 12.1 - - - -
166A GLY* 3.2 22.8 + - - -
189A GLY* 3.5 15.6 - - - -
190A ALA 4.5 2.9 - - - -
191A GLU* 2.8 24.6 + - - -
341A LEU 2.9 0.6 + - - -
342A LEU* 1.3 71.0 - - - +
344A ALA* 1.3 55.9 + - - +
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Residues in contact with ALA 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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189A GLY* 3.6 26.5 - - - +
190A ALA* 4.0 2.2 - - - -
191A GLU* 4.1 2.1 - - - +
234A GLY 3.6 24.2 - - - +
235A ALA* 3.8 7.9 - - - +
341A LEU* 2.9 17.2 + - + +
343A GLY* 1.3 76.5 - - - +
345A ALA* 1.3 65.3 + - - +
346A GLY 3.4 1.6 - - - -
347A ALA* 3.2 4.8 + - - +
348A VAL* 3.0 25.3 + - - +
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Residues in contact with ALA 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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163A CYS 4.6 3.6 - - - +
335A LYS* 4.0 3.4 - - - +
340A HIS* 3.7 26.0 - - + +
341A LEU* 3.5 16.2 + - + +
342A LEU 3.1 15.9 + - - +
344A ALA* 1.3 78.0 - - - +
346A GLY* 1.3 62.4 + - - +
348A VAL* 3.3 4.6 - - - +
349A GLU* 3.0 47.1 + - - +
397A SER* 5.0 1.6 - - - +
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Residues in contact with GLY 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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163A CYS 4.6 1.4 + - - -
166A GLY* 4.0 9.4 - - - -
167A VAL* 3.7 31.6 - - - +
170A ILE* 4.0 1.6 - - - +
342A LEU 4.5 1.6 + - - -
344A ALA 3.4 0.4 - - - -
345A ALA* 1.3 78.6 - - - +
347A ALA* 1.3 58.3 + - - +
349A GLU* 4.1 5.5 - - - -
350A SER* 2.8 28.8 + - - -
395A CYS* 4.3 1.0 - - - -
397A SER* 3.9 10.0 + - - -
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Residues in contact with ALA 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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166A GLY* 3.7 6.7 - - - -
170A ILE* 3.8 10.5 - - + -
188A GLY* 3.8 9.2 - - - -
189A GLY 3.6 17.5 - - - +
236A GLY* 3.3 30.5 - - - +
238A LEU* 4.0 2.8 - - + +
344A ALA 3.2 9.3 + - - +
346A GLY* 1.3 75.0 - - - +
348A VAL* 1.3 65.0 + - - +
350A SER* 3.3 12.3 + - - -
351A ILE* 3.4 17.0 + - - +
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Residues in contact with VAL 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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12A MET* 4.1 12.3 - - - -
13A LEU 4.7 2.5 - - - +
14A SER* 5.2 0.9 - - - -
235A ALA 4.0 6.5 - - - +
236A GLY* 3.7 22.9 - - - +
338A THR* 5.5 3.4 - - + -
341A LEU* 4.2 24.5 - - + -
344A ALA 3.0 13.5 + - - +
345A ALA* 3.3 16.6 - - - +
347A ALA* 1.3 74.5 - - - +
349A GLU* 1.3 67.8 + - + +
351A ILE* 3.2 12.9 + - - +
352A TYR* 3.1 54.0 + - + +
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Residues in contact with GLU 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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301A ASN* 2.9 30.0 + - - +
302A ALA 3.8 3.3 - - - +
334A THR* 4.0 14.9 + - - +
335A LYS* 2.5 47.7 + - - +
338A THR* 5.3 2.5 - - + +
345A ALA* 3.0 25.5 + - - +
348A VAL* 1.3 81.0 - - + +
350A SER* 1.3 60.6 + - - +
352A TYR* 3.6 9.9 - - + +
353A SER* 2.8 31.0 + - - -
395A CYS* 3.8 11.7 - - - -
396A ASN 4.1 8.5 - - - +
397A SER* 4.8 2.3 + - - -
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Residues in contact with SER 350 (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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170A ILE* 3.5 20.2 - - - +
238A LEU* 4.6 5.2 - - - -
346A GLY 2.8 22.7 + - - -
347A ALA 3.3 6.9 + - - -
349A GLU* 1.3 73.7 - - - +
351A ILE* 1.3 60.0 + - - +
353A SER* 3.3 7.7 + - - -
354A ILE* 2.9 35.0 + - - +
395A CYS* 4.2 6.5 - - - -
407A LEU* 3.7 15.6 - - - +
409A PHE* 3.9 18.5 - - - -
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Residues in contact with ILE 351 (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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10A LEU* 4.0 20.4 - - + -
11A GLY 3.5 28.9 - - - +
12A MET* 3.4 29.6 - - + -
20A VAL* 4.0 2.9 - - + -
236A GLY* 4.1 4.5 - - - -
237A MET 4.0 8.1 - - - +
238A LEU* 3.3 30.1 - - + -
347A ALA 3.5 9.6 - - - +
348A VAL* 3.2 8.0 + - - +
350A SER* 1.3 73.8 - - - +
352A TYR* 1.3 55.5 + - - +
354A ILE* 2.9 9.2 + - - +
355A LEU* 2.7 50.0 + - + +
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Residues in contact with TYR 352 (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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12A MET* 3.8 24.0 - - + -
14A SER* 4.3 3.6 - - - -
23A THR* 3.8 17.3 - - + +
24A TRP* 3.8 26.1 - + + -
27A LEU* 3.5 28.3 - - + +
299A TYR* 4.9 3.1 - - - +
301A ASN* 4.2 7.2 - - - +
334A THR* 3.3 31.6 - - + -
338A THR* 3.9 20.5 + - + -
348A VAL* 3.1 42.0 + - + +
349A GLU* 3.6 13.9 - - + +
350A SER 3.4 0.2 - - - -
351A ILE* 1.3 76.3 - - + +
353A SER* 1.3 55.3 + - - +
355A LEU* 3.4 0.8 + - + -
356A ALA* 2.9 31.8 + - - +
363A PRO* 5.0 2.5 - - + -
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Residues in contact with SER 353 (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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299A TYR* 4.5 6.9 - - - -
301A ASN* 3.4 21.0 - - - +
349A GLU 2.8 22.7 + - - -
350A SER* 3.5 8.7 - - - -
351A ILE 3.2 0.2 - - - -
352A TYR* 1.3 76.0 - - - +
354A ILE* 1.3 61.9 + - - +
356A ALA* 3.8 4.6 - - - +
357A LEU* 3.6 12.3 + - - +
393A THR* 3.1 34.8 + - - +
394A LEU 4.4 1.2 + - - -
395A CYS* 3.6 14.3 - - - +
409A PHE* 4.4 7.0 - - - -
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Residues in contact with ILE 354 (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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7A VAL* 3.9 24.5 - - + -
10A LEU* 4.4 12.1 - - + -
238A LEU* 4.1 7.6 - - + -
254A TYR* 3.7 42.7 - - + +
255A ALA* 4.3 5.6 - - + -
350A SER 2.9 23.5 + - - +
351A ILE* 2.9 6.9 + - - +
353A SER* 1.3 73.3 - - - +
355A LEU* 1.3 65.6 + - - +
357A LEU* 2.9 26.5 + - - +
358A ARG* 3.3 6.4 + - + +
409A PHE* 3.6 39.7 - - + -
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Residues in contact with LEU 355 (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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10A LEU* 4.0 20.2 - - + -
12A MET* 5.1 1.8 - - + -
20A VAL* 3.8 13.5 - - + +
21A GLU* 4.7 1.1 - - - +
24A TRP* 3.5 52.3 - - + +
254A TYR* 4.8 3.6 - - + -
351A ILE* 2.7 40.3 + - + +
352A TYR* 3.9 2.2 - - + +
354A ILE* 1.3 70.7 - - - +
356A ALA* 1.3 61.0 + - - +
358A ARG* 3.0 50.9 + - - +
359A ASP* 3.0 17.2 + - - +
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Residues in contact with ALA 356 (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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24A TRP* 3.7 6.2 - - + -
299A TYR* 4.1 24.2 - - + -
352A TYR 2.9 18.8 + - - +
353A SER 3.8 7.6 - - - +
354A ILE 3.2 0.2 + - - -
355A LEU* 1.3 75.6 - - - +
357A LEU* 1.3 57.6 + - - +
360A GLN* 2.9 30.1 + - - -
361A ALA 3.5 22.9 + - - +
362A VAL* 4.8 0.4 - - + -
363A PRO* 4.8 0.7 - - + -
390A MET* 3.5 14.4 - - + +
393A THR* 4.7 0.2 - - + -
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Residues in contact with LEU 357 (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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254A TYR 5.6 3.4 - - - +
255A ALA* 4.6 6.3 - - + -
353A SER 3.6 10.8 - - - +
354A ILE* 2.9 10.3 + - - +
356A ALA* 1.3 76.1 - - - +
358A ARG* 1.3 60.2 + - - +
360A GLN* 3.0 26.0 + - - +
390A MET* 3.8 19.3 - - + +
391A GLU* 3.6 26.7 - - - +
392A TYR 4.0 0.2 - - - +
393A THR* 3.7 33.2 - - + +
409A PHE* 4.0 19.1 - - + +
410A LYS 4.0 1.8 - - - -
411A LYS* 3.8 41.6 - - + +
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Residues in contact with ARG 358 (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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21A GLU* 2.7 42.4 + - - -
24A TRP* 3.9 4.8 - - - -
254A TYR* 4.4 29.9 + - + +
354A ILE* 3.3 5.8 + - + +
355A LEU* 3.0 34.3 + - + +
357A LEU* 1.3 80.6 - - - +
359A ASP* 1.3 86.4 + - - +
360A GLN* 3.5 2.6 - - - +
411A LYS* 4.3 17.5 + - - +
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Residues in contact with ASP 359 (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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24A TRP* 3.0 32.7 + - + +
28A LEU* 4.8 4.2 - - + +
355A LEU 3.0 9.2 + - - +
358A ARG* 1.3 109.8 + - - +
360A GLN* 1.3 70.7 + - - +
361A ALA* 3.0 15.3 + - + +
386A GLN* 4.5 4.3 + - - -
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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