Contacts of the helix formed by residues 419 - 428 (chain A) in PDB entry 4IKV
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 VAL 419 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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367A ILE* 3.9 34.7 - - + +
370A LYS* 4.0 31.0 - - + +
371A PHE* 3.9 7.4 - - + -
415A CYS 3.6 14.1 - - - +
416A LEU 3.2 13.5 - - - +
418A PRO* 1.3 82.2 - - + +
420A GLY* 1.3 59.4 + - - +
421A LEU 3.5 1.8 - - - -
422A SER* 3.9 9.2 - - - -
423A ALA* 2.9 31.0 + - - +
613A PG4 4.2 17.3 - - - +
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Residues in contact with GLY 420 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371A PHE* 3.9 10.1 - - - -
416A LEU 3.3 3.2 + - - -
417A SER 3.2 6.5 + - - -
418A PRO 3.5 0.2 - - - -
419A VAL* 1.3 79.1 - - - +
421A LEU* 1.3 60.5 + - - +
423A ALA* 3.6 2.8 - - - +
424A THR* 2.8 26.7 + - - -
440A TRP* 3.5 39.6 - - - -
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Residues in contact with LEU 421 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
417A SER 4.6 1.4 + - - -
418A PRO 5.2 1.2 + - - +
420A GLY* 1.3 74.5 - - - +
422A SER* 1.3 58.1 + - - +
424A THR* 3.1 2.6 + - - -
425A THR* 2.8 40.7 + - - +
436A THR* 3.8 15.0 - - - +
437A MET* 3.7 49.4 - - + +
440A TRP* 3.9 25.6 - - + +
441A PHE* 6.5 0.4 - - + -
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Residues in contact with SER 422 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367A ILE* 3.6 8.0 - - - +
418A PRO 5.0 3.5 + - - -
419A VAL* 3.7 18.1 - - - +
420A GLY 3.2 0.4 - - - -
421A LEU* 1.3 79.0 - - - +
423A ALA* 1.3 57.6 + - - +
425A THR* 3.4 5.5 + - - +
426A LYS* 2.9 59.2 + - - +
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Residues in contact with ALA 423 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295A TYR* 4.2 3.8 - - + -
298A LEU* 4.0 6.3 - - + -
367A ILE* 3.6 21.2 - - + +
371A PHE* 3.7 16.4 - - + -
419A VAL 2.9 18.9 + - - +
420A GLY 3.6 5.2 - - - +
422A SER* 1.3 75.7 - - - +
424A THR* 1.3 62.0 + - - +
426A LYS* 3.4 2.4 + - - +
427A LEU* 3.1 30.1 + - - +
492A MET* 4.0 16.6 - - + -
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Residues in contact with THR 424 (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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295A TYR* 2.7 35.1 + - + +
420A GLY 2.8 17.7 + - - -
421A LEU* 3.1 9.5 + - - -
423A ALA* 1.3 77.6 - - - +
425A THR* 1.3 61.4 + - - +
427A LEU 3.3 0.5 + - - -
428A ALA* 3.0 30.3 + - - +
436A THR* 3.5 28.0 - - + +
439A LEU* 3.7 23.1 - - + -
440A TRP* 3.5 14.5 - - - +
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Residues in contact with THR 425 (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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421A LEU* 2.8 27.7 + - - +
422A SER* 3.9 6.1 - - - -
424A THR* 1.3 79.3 - - - +
426A LYS* 1.3 63.1 + - + +
427A LEU 3.3 0.3 + - - -
428A ALA* 3.7 12.8 + - - +
433A SER* 6.4 1.8 - - - -
436A THR* 3.9 28.5 + - + +
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Residues in contact with LYS 426 (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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291A ARG* 3.8 9.0 + - - -
367A ILE* 3.7 21.5 - - + -
422A SER* 2.9 41.4 + - - +
423A ALA 3.8 4.0 - - - +
424A THR 3.3 0.2 - - - -
425A THR* 1.3 78.5 - - + +
427A LEU* 1.3 59.8 + - - +
428A ALA 3.6 1.4 + - - +
492A MET* 4.3 21.3 - - + -
493A LYS* 3.6 50.2 + - + +
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Residues in contact with LEU 427 (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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288A GLU 4.5 0.5 - - - +
291A ARG* 3.5 59.4 - - + +
292A VAL* 3.7 6.6 + - - +
294A ALA* 4.1 11.2 - - + +
295A TYR* 3.8 40.5 - - + +
298A LEU* 3.9 9.6 - - + -
423A ALA 3.1 12.5 + - - +
424A THR 3.9 0.2 - - - -
426A LYS* 1.3 80.5 - - - +
428A ALA* 1.3 62.0 + - - +
429A PRO* 4.0 1.6 - - - +
488A ILE* 4.4 2.7 - - + +
491A LEU* 4.2 2.5 - - + +
492A MET* 3.6 46.9 - - + +
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Residues in contact with ALA 428 (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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278A MET* 4.7 4.0 - - - -
288A GLU* 4.9 2.3 - - - +
291A ARG* 5.5 2.6 + - - -
292A VAL* 5.2 0.2 - - - -
295A TYR* 6.4 0.7 - - + -
424A THR 3.0 17.7 + - - +
425A THR 3.7 10.0 + - - +
426A LYS 3.6 1.6 - - - +
427A LEU* 1.3 80.8 - - - +
429A PRO* 1.3 75.9 - - + +
430A ALA* 3.6 1.2 + - - -
432A PHE* 5.0 4.5 - - + +
436A THR* 4.2 19.7 - - + -
439A LEU* 4.6 17.5 - - + -
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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
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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