Contacts of the helix formed by residues 345 - 359 (chain A) in PDB entry 5KVI
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 345 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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343A ILE 3.8 0.2 - - - -
344A LEU* 1.3 88.1 - - + +
346A GLU* 1.3 67.5 + - - +
347A TYR* 3.2 5.4 - - + +
348A LEU* 3.0 12.0 + - + +
349A SER 2.9 18.9 + - - -
500A SER* 4.6 8.0 - - - +
504A THR* 3.8 19.5 - - + +
506A GLY* 6.2 0.4 - - - -
508A PHE* 5.3 4.9 - - + -
565A ILE* 3.6 41.3 - - + -
567A TYR* 3.7 11.4 - - + +
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Residues in contact with GLU 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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337A LYS* 3.8 31.0 - - + +
344A LEU 3.7 1.2 + - - -
345A PRO* 1.3 72.9 - - - +
347A TYR* 1.3 64.9 + - - +
349A SER* 3.8 7.8 - - - -
350A ASN* 2.9 28.0 + - + +
500A SER* 5.8 0.4 - - - -
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Residues in contact with TYR 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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345A PRO* 3.2 5.2 - - + +
346A GLU* 1.3 77.6 - - - +
348A LEU* 1.3 70.1 + - + +
350A ASN* 3.6 5.1 + - - +
351A TRP* 3.1 36.0 + + + +
508A PHE* 4.0 28.3 - + + -
559A ASP* 5.3 1.8 + - - +
560A TYR* 3.5 36.3 + + - +
579A TRP* 4.2 25.4 - + - -
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Residues in contact with LEU 348 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344A LEU* 3.9 25.1 - - + -
345A PRO* 3.0 17.4 + - + +
347A TYR* 1.3 86.2 - - + +
349A SER* 1.3 60.2 + - - +
351A TRP* 4.1 11.4 - - + -
352A THR* 2.8 34.8 + - - +
492A TYR* 4.4 4.3 - - + -
508A PHE* 4.9 1.1 - - + -
565A ILE* 3.4 28.5 - - + -
577A VAL* 4.8 0.7 - - + -
579A TRP* 3.6 61.5 - - + +
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Residues in contact with SER 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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338A GLY* 3.0 21.9 + - - -
339A ASN 2.7 28.8 + - - -
341A GLY* 3.6 14.6 - - - -
344A LEU* 4.0 13.1 - - - +
345A PRO 2.9 14.6 + - - -
346A GLU* 3.8 8.1 - - - -
348A LEU* 1.3 77.4 - - - +
350A ASN* 1.3 56.3 + - - +
352A THR* 3.3 4.2 + - - -
353A MET* 3.0 26.7 + - - +
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Residues in contact with ASN 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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338A GLY* 5.5 1.1 - - - -
346A GLU* 2.9 22.1 + - + +
347A TYR* 3.9 4.2 + - - +
349A SER* 1.3 75.2 - - - +
351A TRP* 1.3 67.0 + - - +
353A MET* 3.1 28.3 + - - +
354A GLU* 3.0 34.2 + - - +
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Residues in contact with TRP 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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347A TYR* 3.1 36.4 + + + +
348A LEU* 3.7 11.9 - - + +
349A SER 3.4 0.2 - - - -
350A ASN* 1.3 77.8 - - - +
352A THR* 1.3 67.2 + - - +
354A GLU* 3.3 7.2 + - + +
355A LYS* 2.9 36.6 + - + -
358A ARG* 4.2 22.2 + - - +
490A VAL* 4.0 26.5 - - + -
492A TYR* 3.8 14.1 - - - -
560A TYR 4.4 9.0 + - - -
561A GLY* 5.6 1.8 - - - -
579A TRP* 3.6 45.7 - + - -
580A ASN* 5.1 2.5 - - - -
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Residues in contact with THR 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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313A SER* 5.4 0.4 - - - -
339A ASN* 3.8 15.5 - - + -
340A MET* 3.6 21.8 - - + -
344A LEU* 3.8 6.3 - - - +
348A LEU 2.8 21.9 + - - -
349A SER* 3.5 7.4 - - - -
350A ASN 3.2 0.2 - - - -
351A TRP* 1.3 82.8 - - - +
353A MET* 1.3 65.6 + - - +
355A LYS* 3.1 4.7 + - - +
356A VAL* 2.9 29.0 + - + +
486A LEU* 4.0 13.0 - - + -
492A TYR* 2.8 30.0 + - - +
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Residues in contact with MET 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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337A LYS 3.6 21.5 - - - +
338A GLY* 4.0 7.2 - - - -
339A ASN* 3.1 21.9 + - - +
349A SER 3.0 12.6 + - - +
350A ASN* 3.1 28.5 + - - +
352A THR* 1.3 77.1 - - - +
354A GLU* 1.3 57.8 + - - +
356A VAL* 3.4 3.4 + - - +
357A ARG* 2.9 52.0 + - - +
363A VAL* 3.7 21.0 - - + +
365A PRO* 3.8 29.4 - - + -
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Residues in contact with GLU 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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350A ASN* 3.0 30.2 + - - +
351A TRP* 3.7 9.4 - - + +
353A MET* 1.3 76.8 - - - +
355A LYS* 1.3 60.8 + - - +
357A ARG* 2.8 43.2 + - - +
358A ARG* 2.9 50.0 + - - +
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Residues in contact with LYS 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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317A CYS* 4.2 12.3 - - - -
321A ARG* 4.5 6.3 - - - +
351A TRP* 2.9 30.3 + - + +
352A THR* 3.1 8.7 + - + +
354A GLU* 1.3 75.6 - - - +
356A VAL* 1.3 63.4 + - - +
358A ARG* 3.2 33.8 + - + +
359A GLU* 2.7 38.4 + - - +
486A LEU* 4.1 25.8 - - + -
487A GLY* 5.9 0.6 - - - -
489A ASP* 4.9 10.1 + - - +
490A VAL* 3.6 34.5 - - + +
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Residues in contact with VAL 356 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313A SER* 4.7 5.2 - - - -
316A ALA* 4.0 10.3 - - + -
317A CYS* 4.0 18.4 - - - -
332A GLN* 3.6 19.7 - - - +
339A ASN* 3.8 16.8 - - - +
352A THR* 2.9 24.2 + - + +
353A MET 3.7 4.7 - - - +
355A LYS* 1.3 76.4 - - - +
357A ARG* 1.3 61.7 + - - +
359A GLU* 3.1 21.3 + - - +
361A VAL* 3.5 22.3 - - + +
363A VAL* 3.7 14.6 - - + -
486A LEU* 4.5 5.6 - - + -
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Residues in contact with ARG 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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324A ARG* 5.0 0.5 + - - -
353A MET* 2.9 38.2 + - - +
354A GLU* 2.8 47.5 + - - +
356A VAL* 1.3 76.5 - - - +
358A ARG* 1.3 59.5 + - + +
360A GLY* 3.0 19.9 + - - -
361A VAL 3.4 20.1 + - - +
362A LYS* 5.2 0.4 - - - -
363A VAL* 3.0 38.4 + - + +
365A PRO* 3.7 17.4 - - - +
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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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324A ARG* 3.0 23.7 + - - -
351A TRP* 4.2 22.4 - - - +
354A GLU* 2.9 34.0 + - + +
355A LYS* 3.2 37.3 + - - +
357A ARG* 1.3 75.7 - - + +
359A GLU* 1.3 58.7 + - + +
360A GLY 3.1 1.9 + - - -
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Residues in contact with GLU 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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317A CYS* 4.1 17.5 - - - +
320A GLY* 3.6 22.2 - - - +
321A ARG* 2.7 49.3 + - - +
324A ARG* 3.7 18.5 + - - +
355A LYS* 2.7 39.2 + - - +
356A VAL* 3.1 11.3 + - - +
358A ARG* 1.3 78.8 - - - +
360A GLY* 1.3 58.9 + - - +
361A VAL* 3.4 8.9 + - + -
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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