Contacts of the helix formed by residues 276 - 285 (chain I) in PDB entry 2VKZ
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 GLY 276 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160I PHE* 3.3 17.1 - - - +
161I GLY 3.0 24.1 + - - -
245I GLN* 4.1 5.6 - - - -
272I GLY* 3.3 7.2 - - - -
273I HIS 2.9 9.7 + - - -
275I GLN* 1.3 76.2 - - - +
277I LEU* 1.3 66.1 + - - +
278I VAL 3.2 0.7 - - - -
279I THR* 3.1 20.2 + - - -
280I ALA 3.4 2.3 + - - -
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Residues in contact with LEU 277 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272I GLY* 3.3 24.6 - - - +
274I SER 3.3 14.6 + - - +
276I GLY* 1.3 76.9 - - - +
278I VAL* 1.3 63.9 + - - +
280I ALA* 3.0 12.1 + - - +
281I VAL* 3.1 17.0 + - + +
459I VAL* 4.3 4.9 - - + -
460I TYR 5.0 5.8 - - - +
462I THR* 3.7 26.9 - - - +
468I LEU* 3.8 17.7 - - + -
479I ILE* 3.4 43.7 - - + +
482I CYS* 4.0 20.9 - - + -
483I ILE* 4.5 4.3 - - + -
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Residues in contact with VAL 278 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275I GLN 3.6 3.1 + - - +
276I GLY 3.2 0.2 - - - -
277I LEU* 1.3 78.7 - - - +
279I THR* 1.3 63.3 + - - +
281I VAL* 3.2 4.7 + - - +
282I ALA* 3.0 20.1 + - - +
299I ALA* 3.6 26.5 - - + +
302I VAL* 3.8 24.0 - - + -
303I LEU* 3.5 36.8 - - + -
306I ILE* 4.2 1.8 - - + -
450I PHE* 5.3 3.6 - - + -
479I ILE* 4.2 20.0 - - + -
483I ILE* 3.7 24.0 - - + -
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Residues in contact with THR 279 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160I PHE* 3.3 25.5 - - - +
242I GLY* 4.2 15.0 - - - +
245I GLN* 3.5 22.4 + - + +
246I LEU* 4.0 25.7 - - + +
275I GLN 5.3 1.3 - - - +
276I GLY 3.1 14.1 + - - +
278I VAL* 1.3 76.3 - - + +
280I ALA* 1.3 52.3 + - - +
282I ALA* 3.6 7.5 - - - +
283I ILE* 2.7 38.3 + - - +
299I ALA* 4.6 9.6 - - + -
303I LEU* 4.7 7.9 - - + -
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Residues in contact with ALA 280 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160I PHE* 3.6 27.4 - - + -
270I ALA* 4.1 4.3 - - + +
271I THR* 3.7 33.7 - - - +
272I GLY 3.8 1.1 - - - +
276I GLY 3.4 1.1 + - - +
277I LEU 3.0 9.5 + - - +
279I THR* 1.3 77.1 + - - +
281I VAL* 1.3 69.5 + - - +
283I ILE* 3.1 19.0 - - - +
284I ALA* 3.2 6.9 + - - +
459I VAL* 4.1 7.7 - - + +
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Residues in contact with VAL 281 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277I LEU* 3.1 7.5 + - + +
278I VAL 3.4 7.9 - - - +
280I ALA* 1.3 81.1 - - - +
282I ALA* 1.3 65.3 + - - +
284I ALA* 3.1 12.0 + - - +
285I GLU* 3.4 11.8 + - - +
450I PHE* 3.3 46.9 - - + -
455I ILE* 5.1 8.5 - - + +
459I VAL* 3.6 28.7 - - + +
468I LEU* 3.9 15.7 - - + -
475I ILE* 4.4 9.9 - - + -
479I ILE* 4.1 15.9 - - + -
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Residues in contact with ALA 282 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246I LEU* 5.9 1.8 - - + -
278I VAL 3.0 13.1 + - - +
279I THR* 3.9 2.9 - - - +
281I VAL* 1.3 82.7 - - - +
283I ILE* 1.3 62.3 + - - +
285I GLU* 3.4 7.9 + - - +
286I THR* 3.9 1.2 + - - -
295I SER* 2.9 36.7 + - - +
299I ALA* 3.7 28.5 - - + -
450I PHE* 4.1 17.9 - - + -
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Residues in contact with ILE 283 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160I PHE* 4.2 15.5 - - + -
246I LEU* 4.0 25.8 - - + -
249I TYR* 3.3 62.4 - - + +
264I ARG* 4.0 4.9 - - + +
267I LEU* 5.1 7.4 - - + -
270I ALA* 4.5 9.2 - - + -
279I THR 2.7 18.6 + - - +
280I ALA* 3.1 17.7 - - - +
281I VAL 3.2 0.2 - - - -
282I ALA* 1.3 74.4 - - - +
284I ALA* 1.3 66.6 + - + +
286I THR* 3.0 31.5 - - + +
292I PHE* 4.8 7.9 - - + -
457I ILE* 5.2 0.2 - - + -
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Residues in contact with ALA 284 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264I ARG* 3.3 20.2 - - - +
270I ALA* 5.8 0.2 - - + -
280I ALA 3.7 7.0 - - - +
281I VAL 3.1 10.1 + - - +
283I ILE* 1.3 76.7 - - + +
285I GLU* 1.3 57.8 + - - +
286I THR 3.0 8.6 + - - -
455I ILE* 4.3 4.0 - - + -
456I GLN* 3.2 27.7 + - - +
457I ILE* 3.5 37.9 - - + +
459I VAL* 4.2 5.8 - - + -
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Residues in contact with GLU 285 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264I ARG* 5.2 0.7 - - - -
281I VAL 3.4 6.1 + - - +
282I ALA 3.4 11.8 + - - +
283I ILE 3.3 0.4 - - - -
284I ALA* 1.3 76.9 - - - +
286I THR* 1.3 58.8 + - - +
287I ASP* 3.9 2.4 + - - +
291I SER* 5.4 2.8 + - - -
295I SER* 3.9 11.7 + - - +
298I LYS* 3.2 40.8 + - - +
450I PHE* 3.3 35.9 - - + +
451I ASN 3.9 0.9 + - - +
454I ASP* 3.8 44.0 - - + +
455I ILE* 4.1 7.0 - - + +
456I GLN* 5.6 0.7 - - - -
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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
------------------------------------------------------------
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