Contacts of the helix formed by residues 269 - 278 (chain A) in PDB entry 2VK8
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 LYS 269 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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260A GLY 5.7 0.6 + - - -
262A VAL 5.0 1.6 + - - -
267A LEU 3.9 0.8 + - - -
268A SER* 1.3 72.5 - - - +
270A PRO* 1.3 75.0 - - + +
271A GLU* 4.4 9.5 + - - +
272A VAL* 2.9 39.8 + - + +
273A LYS* 2.9 11.4 + - - +
350A PRO* 5.2 2.2 - - - +
351A ALA 3.1 26.5 + - - -
352A ARG* 4.2 0.6 - - - +
353A THR* 3.4 32.5 + - - +
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Residues in contact with PRO 270 (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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268A SER 3.4 6.2 - - - +
269A LYS* 1.3 85.1 - - + +
271A GLU* 1.3 62.7 + - + +
273A LYS* 3.5 9.8 + - + +
274A GLU* 3.1 25.8 + - - +
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Residues in contact with GLU 271 (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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269A LYS* 3.1 10.1 + - + +
270A PRO* 1.3 80.8 - - + +
272A VAL* 1.3 58.5 + - + +
274A GLU* 4.0 4.0 - - - +
275A ALA* 3.1 29.3 + - - +
350A PRO* 3.5 20.1 - - + +
351A ALA* 3.5 28.6 + - - +
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Residues in contact with VAL 272 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243A PHE* 3.9 20.4 - - + -
260A GLY 3.5 22.7 - - - +
261A GLY* 4.3 6.7 - - - -
262A VAL 3.5 28.0 - - - +
263A TYR* 4.0 10.3 - - + -
268A SER* 4.2 4.7 - - - -
269A LYS* 2.9 32.9 + - + +
271A GLU* 1.3 74.1 - - - +
273A LYS* 1.3 66.4 + - - +
275A ALA* 3.3 1.6 + - - +
276A VAL* 3.0 23.9 + - - +
350A PRO* 4.0 12.6 - - + -
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Residues in contact with LYS 273 (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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263A TYR* 4.2 6.5 - - + -
265A GLY 3.8 11.7 - - - +
266A THR* 4.4 28.7 - - + +
268A SER* 3.8 14.5 - - - +
269A LYS 2.9 14.2 + - - +
270A PRO* 3.7 10.5 - - + +
272A VAL* 1.3 76.1 - - - +
274A GLU* 1.3 60.1 + - - +
276A VAL* 3.8 0.7 - - - +
277A GLU* 2.8 73.4 + - - +
298A SER 6.0 0.9 - - - -
300A SER* 5.1 3.6 - - - -
302A LYS* 4.3 6.7 - - - +
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Residues in contact with GLU 274 (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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270A PRO 3.1 15.6 + - - +
271A GLU* 4.1 4.3 - - - +
273A LYS* 1.3 78.8 + - - +
275A ALA* 1.3 61.1 + - - +
277A GLU* 4.9 3.6 - - - +
278A SER* 2.9 54.7 + - - +
302A LYS* 5.7 2.1 + - - -
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Residues in contact with ALA 275 (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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213A ASN* 4.3 2.9 + - - +
215A VAL* 3.9 12.8 - - - +
243A PHE* 3.7 24.0 - - + -
271A GLU 3.1 19.5 + - - +
272A VAL 3.3 2.0 + - - +
274A GLU* 1.3 78.0 - - - +
276A VAL* 1.3 61.0 + - - +
278A SER* 3.4 14.3 + - - -
279A ALA 3.9 3.6 + - - -
348A ALA 5.6 2.9 - - - +
350A PRO* 3.7 15.9 - - + -
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Residues in contact with VAL 276 (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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215A VAL* 4.6 14.6 - - + -
217A LEU* 5.0 7.0 - - + -
243A PHE* 3.6 36.6 - - + -
263A TYR* 3.8 37.0 - - + -
272A VAL 3.0 16.5 + - - +
273A LYS 3.9 0.2 - - - +
275A ALA* 1.3 76.4 - - - +
277A GLU* 1.3 62.4 + - - +
279A ALA* 3.1 22.7 + - - +
282A ILE* 4.1 6.4 - - + +
301A TYR* 3.9 25.6 - - + -
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Residues in contact with GLU 277 (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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263A TYR* 2.7 32.2 + - + +
265A GLY* 4.4 2.3 - - - -
273A LYS* 2.8 63.6 + - - +
274A GLU* 4.6 4.3 - - - +
276A VAL* 1.3 73.3 - - - +
278A SER* 1.3 59.7 + - - +
279A ALA 3.2 2.7 + - - +
282A ILE* 6.0 0.2 - - - -
298A SER 4.4 2.1 - - - +
299A TYR* 4.1 1.2 - - - -
300A SER* 3.1 38.2 + - - +
301A TYR* 4.2 7.4 - - + +
302A LYS* 3.1 45.7 + - - +
303A THR* 5.8 0.2 - - - +
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Residues in contact with SER 278 (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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213A ASN* 3.0 24.2 + - - +
274A GLU* 2.9 41.8 + - - +
275A ALA* 3.4 8.0 + - - -
276A VAL 3.2 0.2 - - - -
277A GLU* 1.3 73.7 - - - +
279A ALA* 1.3 67.4 + - - +
280A ASP* 3.6 1.7 + - - +
302A LYS* 5.1 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