Contacts of the strand formed by residues 267 - 272 (chain H) 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 LEU 267 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156H LEU* 3.4 21.5 - - + +
158H ALA* 3.6 32.8 - - + +
249H TYR* 4.9 11.2 - - + +
263H LEU* 3.3 23.1 - - + +
264H ARG* 3.3 19.6 - - + +
265H SER 3.0 4.8 - - - +
266H TYR* 1.3 83.5 - - + +
268H LYS* 1.3 62.8 + - - +
269H GLY 3.0 11.3 + - - +
270H ALA* 4.7 0.9 - - + -
283H ILE* 5.1 2.5 - - + -
457H ILE* 3.4 41.3 - - + +
502H LEU* 6.2 2.0 - - + -
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Residues in contact with LYS 268 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155H GLN* 4.5 25.0 + - + +
156H LEU 2.8 14.4 + - - +
157H VAL* 4.4 9.9 - - + -
266H TYR 3.8 2.6 + - - -
267H LEU* 1.3 71.2 - - - +
269H GLY* 1.3 55.3 + - - +
457H ILE* 5.0 0.2 - - - -
458H PRO* 3.3 22.8 - - - +
460H TYR* 3.9 17.2 + - - +
496H PHE* 4.6 3.1 - - - +
497H LYS* 3.2 40.5 + - - +
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Residues in contact with GLY 269 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156H LEU 3.9 0.2 + - - -
157H VAL* 3.3 13.1 - - - +
158H ALA 3.2 19.4 + - - -
267H LEU* 3.0 7.4 - - - +
268H LYS* 1.3 81.2 - - - +
270H ALA* 1.3 61.8 + - - +
457H ILE* 4.0 9.9 - - - -
458H PRO* 3.4 19.1 - - - -
460H TYR* 4.2 7.6 - - - -
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Residues in contact with ALA 270 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157H VAL* 4.3 2.2 - - - -
158H ALA* 3.1 28.5 - - + +
269H GLY* 1.3 73.8 - - - +
271H THR* 1.3 70.5 + - - +
280H ALA* 4.1 19.3 - - + +
283H ILE* 4.5 9.9 - - + -
457H ILE* 4.2 12.0 - - + +
458H PRO 2.9 18.8 + - - +
459H VAL* 3.2 10.6 - - + -
460H TYR* 3.2 4.6 + - - -
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Residues in contact with THR 271 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157H VAL* 5.6 0.7 - - - -
158H ALA 2.9 5.9 + - - +
159H ILE* 3.2 11.4 - - - +
160H PHE* 2.9 20.6 + - - -
270H ALA* 1.3 80.2 + - - +
272H GLY* 1.3 73.8 + - - +
280H ALA* 3.7 10.5 - - - +
459H VAL* 4.8 2.7 - - - -
460H TYR* 2.8 45.3 + - - +
490H TRP* 4.0 14.4 - - + -
493H THR* 3.9 19.1 - - - +
494H THR* 6.0 0.2 - - - -
496H PHE* 5.1 8.5 - - + -
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Residues in contact with GLY 272 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160H PHE 3.3 10.1 - - - -
271H THR* 1.3 87.0 - - - +
273H HIS* 1.3 60.9 + - - -
274H SER 4.1 0.2 - - - -
276H GLY 3.3 5.2 - - - -
277H LEU* 3.3 34.9 + - - +
280H ALA* 3.8 0.4 - - - +
462H THR* 3.6 15.8 + - - -
490H TRP* 3.5 7.9 - - - -
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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
------------------------------------------------------------
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