Contacts of the helix formed by residues 348 - 364 (chain A) in PDB entry 2VWK
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 SER 348 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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266A ARG* 4.5 5.6 - - - +
346A ARG 3.8 1.8 + - - -
347A SER* 1.3 76.9 + - - +
349A THR* 1.3 65.1 + - - +
350A GLY* 3.9 3.3 + - - -
351A ASN* 3.2 14.1 + - - +
352A LEU* 3.0 22.2 + - - +
499A TYR* 4.0 3.2 + - - -
1779A SO4 2.7 38.3 + - - -
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Residues in contact with THR 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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266A ARG* 4.2 21.7 - - + +
348A SER* 1.3 74.2 - - - +
350A GLY* 1.3 64.5 + - - +
352A LEU* 3.2 17.4 + - + +
353A VAL* 3.0 26.3 + - - +
488A ILE* 5.0 9.4 - - + -
492A SER* 3.3 30.4 + - - +
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Residues in contact with GLY 350 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348A SER* 3.3 4.1 + - - -
349A THR* 1.3 83.6 + - - +
351A ASN* 1.3 59.7 + - - +
353A VAL* 3.4 2.8 + - - -
354A GLU* 3.2 18.4 + - - +
492A SER* 5.0 1.1 - - - -
495A GLY 5.8 0.4 - - - -
496A TYR* 3.5 25.2 - - - -
499A TYR* 3.7 27.0 - - - -
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Residues in contact with ASN 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 SER* 2.6 27.2 + - - +
348A SER* 3.2 20.4 + - - +
350A GLY* 1.3 75.7 - - - +
352A LEU* 1.3 61.9 + - - +
354A GLU* 3.3 13.1 + - - +
355A TRP* 3.1 56.0 + - - -
499A TYR* 3.9 10.5 + - - +
1779A SO4 4.0 10.8 + - - +
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Residues in contact with LEU 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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266A ARG* 5.2 3.6 - - - -
333A LEU* 4.8 18.6 - - + -
337A VAL* 3.6 22.1 - - + +
344A VAL* 3.5 49.8 - - + +
347A SER* 3.6 15.7 + - - +
348A SER 3.0 22.7 + - - +
349A THR* 3.2 22.4 + - + +
351A ASN* 1.3 72.4 - - - +
353A VAL* 1.3 64.8 + - - +
355A TRP* 3.6 5.7 + - + -
356A PHE* 3.2 22.0 + - - +
488A ILE* 5.0 8.5 - - + -
489A LEU* 4.1 8.1 - - + -
492A SER* 5.7 0.9 - - - +
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Residues in contact with VAL 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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349A THR 3.0 8.5 + - - +
350A GLY 3.5 8.1 - - - +
351A ASN 3.2 0.2 - - - -
352A LEU* 1.3 75.4 - - - +
354A GLU* 1.3 52.0 + - - +
356A PHE* 3.1 3.9 + - - +
357A LEU* 2.7 46.5 + - + +
489A LEU* 3.8 21.8 - - + +
492A SER* 3.5 40.6 - - - +
493A PHE* 4.2 16.4 - - + -
496A TYR* 3.4 35.4 - - + -
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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 GLY 3.2 12.8 + - - +
351A ASN* 3.3 20.4 + - - +
353A VAL* 1.3 77.5 - - - +
355A TRP* 1.3 59.5 + - + +
357A LEU* 3.7 2.2 - - - +
358A LEU* 2.8 40.6 + - + +
371A LYS* 5.7 2.7 - - - +
496A TYR* 2.4 28.5 + - - -
499A TYR* 5.0 3.0 - - + -
501A LYS 3.8 4.5 - - - +
502A ALA* 3.4 8.8 - - - -
503A ARG* 2.7 53.2 + - - +
504A TRP* 3.5 9.4 - - - -
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Residues in contact with TRP 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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115A PRO* 6.2 1.2 - - - +
118A LYS* 3.7 32.3 - - + +
122A ILE* 4.9 2.8 - - + +
337A VAL* 3.4 29.8 - - + +
339A GLN* 3.8 31.7 + - + +
343A ASP* 3.7 35.4 - - + -
344A VAL* 4.2 3.8 - - + -
347A SER* 3.3 26.2 - - - -
351A ASN* 3.1 37.7 + - - +
352A LEU* 4.5 2.7 - - - -
353A VAL 3.3 0.2 - - - -
354A GLU* 1.3 77.3 - - + +
356A PHE* 1.3 64.5 + - - +
358A LEU* 3.6 17.4 + - + +
359A ARG* 3.4 18.7 + - - +
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Residues in contact with PHE 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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336A LEU* 3.5 28.3 - - + -
337A VAL* 4.0 11.1 - - + +
352A LEU 3.2 14.6 + - - +
353A VAL 3.1 8.2 + - - +
355A TRP* 1.3 76.9 - - - +
357A LEU* 1.3 68.2 + - + +
359A ARG* 3.5 5.3 + - + +
360A LYS* 3.2 60.6 + - + +
452A LEU* 4.3 16.8 - - + -
456A LEU* 4.1 25.8 - - + -
489A LEU* 3.6 28.0 - - + -
493A PHE* 4.1 25.6 - + - -
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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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353A VAL* 2.7 29.4 + - + +
354A GLU 3.7 2.5 - - - +
356A PHE* 1.3 75.1 - - + +
358A LEU* 1.3 55.2 + - - +
360A LYS* 3.4 3.1 + - - +
361A ALA* 2.7 38.4 + - - +
448A PHE* 3.9 4.6 - - + -
449A ILE* 3.7 25.1 - - + -
452A LEU* 3.6 27.1 - - + -
493A PHE* 4.1 13.9 - - + -
496A TYR* 3.5 41.5 - - + +
504A TRP* 3.6 23.1 - - + -
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Residues in contact with LEU 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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111A GLU* 5.3 2.9 - - - +
114A ILE* 3.9 34.5 - - + -
119A ARG* 4.9 4.8 + - - +
122A ILE* 3.8 22.3 - - + +
354A GLU* 2.8 27.0 + - + +
355A TRP* 4.0 16.6 - - + +
356A PHE 3.4 0.2 - - - -
357A LEU* 1.3 75.9 - - - +
359A ARG* 1.3 61.8 + - - +
361A ALA* 3.3 6.2 - - + +
362A TYR* 3.1 20.4 + - - +
368A ALA* 3.6 31.2 - - + -
503A ARG* 4.2 20.0 - - - +
504A TRP* 4.3 4.9 - - + -
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Residues in contact with ARG 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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121A LEU* 3.1 27.3 + - - +
122A ILE* 3.7 29.5 + - + +
125A GLY* 3.3 21.4 + - - -
126A LEU 2.6 29.1 + - - -
127A ILE* 4.2 9.9 - - - +
336A LEU 5.9 0.7 - - - +
337A VAL 4.2 7.8 + - - +
338A GLY* 2.9 40.1 + - - -
339A GLN* 4.5 1.0 - - - +
355A TRP 3.4 12.5 + - - +
356A PHE* 4.2 8.1 - - + +
357A LEU 3.2 0.8 - - - -
358A LEU* 1.3 75.0 - - - +
360A LYS* 1.3 75.1 + - + +
362A TYR* 3.0 15.4 + - - +
363A GLU* 3.2 34.1 + - - +
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Residues in contact with LYS 360 (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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356A PHE* 3.2 51.0 + - + +
357A LEU 3.8 2.9 - - - +
359A ARG* 1.3 80.2 - - + +
361A ALA* 1.3 57.2 + - - +
363A GLU* 3.1 28.7 + - - +
364A ARG* 2.9 36.9 + - + +
448A PHE* 4.3 0.2 - - - -
452A LEU* 3.8 36.2 - - + +
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Residues in contact with ALA 361 (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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111A GLU* 5.9 0.4 - - - +
357A LEU 2.7 22.8 + - - +
358A LEU* 3.3 13.9 - - + +
360A LYS* 1.3 72.4 - - - +
362A TYR* 1.3 61.5 + - - +
364A ARG 3.5 0.2 + - - -
365A ASN* 3.1 3.3 + - - -
366A GLU* 2.8 49.4 + - + +
368A ALA* 5.2 0.9 - - + -
448A PHE* 3.7 19.2 - - + -
504A TRP* 4.1 11.9 - - + -
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Residues in contact with TYR 362 (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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37A TYR* 3.8 8.5 - + - -
39A TYR* 5.3 6.1 - - - -
73A LYS* 5.9 4.7 + - - +
84A LYS* 5.6 4.5 + - - -
111A GLU* 5.9 0.7 - - - -
119A ARG* 4.0 9.0 - - - +
122A ILE* 3.5 23.3 - - + -
123A ASP* 3.4 61.0 + - - +
358A LEU 3.1 5.5 + - - +
359A ARG 3.0 11.5 + - - +
361A ALA* 1.3 77.2 - - - +
363A GLU* 1.3 69.1 + - + +
365A ASN* 3.3 12.0 + - - +
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Residues in contact with GLU 363 (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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122A ILE 6.0 1.1 - - - +
125A GLY* 6.1 0.2 - - - -
359A ARG* 3.4 37.6 + - - +
360A LYS* 3.1 36.8 + - - +
362A TYR* 1.3 82.5 - - + +
364A ARG* 1.3 61.9 + - + +
365A ASN* 3.2 1.6 + - - +
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Residues in contact with ARG 364 (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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74A LYS* 3.0 30.0 + - - +
360A LYS* 2.9 25.1 + - + +
361A ALA 3.5 3.1 + - - +
363A GLU* 1.3 78.1 - - + +
365A ASN* 1.3 64.9 + - - +
366A GLU* 3.3 6.7 + - + +
448A PHE* 3.7 37.5 + - + +
451A SER* 2.4 34.8 + - - -
452A LEU* 4.0 18.9 - - - +
455A ASP* 5.7 1.6 + - - -
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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