Contacts of the helix formed by residues 279 - 284 (chain D) in PDB entry 5WYF
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 279 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115D GLY 4.9 2.9 - - - -
251D GLU 5.0 0.2 + - - -
252D VAL* 3.8 19.1 - - - +
256D LEU* 4.1 5.5 - - - +
278D VAL* 1.3 78.4 - - - +
280D LYS* 1.3 66.5 + - - +
281D SER 2.7 12.1 + - - -
282D LEU* 3.2 12.3 + - - +
288D LEU 3.7 17.0 - - - -
289D SER* 4.3 4.3 - - - -
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Residues in contact with LYS 280 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309C THR* 2.6 41.6 + - + +
310C THR* 4.9 11.5 - - - +
54D ALA* 2.9 41.0 + - - +
55D SER 3.9 7.4 - - - +
56D ALA* 3.6 11.9 - - - -
252D VAL* 3.3 28.9 - - + +
253D ASN* 3.7 11.7 - - - +
279D GLY* 1.3 68.9 - - - +
281D SER* 1.3 62.9 + - - +
282D LEU* 3.2 2.4 + - - +
283D ALA 4.0 2.8 + - - -
285D GLY* 3.5 22.0 + - - -
286D MET 4.8 2.9 - - - +
288D LEU 4.4 4.1 + - - +
1001D ILP 3.2 46.2 + - - +
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Residues in contact with SER 281 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55D SER 2.7 21.2 + - - -
56D ALA* 3.3 9.4 - - - +
58D ASN* 2.8 48.3 + - - +
252D VAL 4.9 0.6 + - - -
255D GLY 5.5 0.2 - - - -
256D LEU* 3.5 15.3 - - - +
279D GLY 2.7 6.1 + - - -
280D LYS* 1.3 73.9 - - - +
282D LEU* 1.3 62.2 + - - -
283D ALA 3.2 1.8 + - - -
284D SER* 3.4 3.8 + - - -
323D THR* 3.3 21.3 - - - +
327D ILE* 5.3 0.2 - - - +
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Residues in contact with LEU 282 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93D LEU* 4.7 0.2 - - + -
97D LEU* 3.6 39.5 - - + -
256D LEU* 3.2 15.9 - - + +
278D VAL* 4.0 16.6 - - + -
279D GLY 3.2 16.6 + - - +
280D LYS 3.2 0.8 - - - -
281D SER* 1.3 77.6 - - - +
283D ALA* 1.3 55.4 + - - +
288D LEU* 3.6 45.8 - - + +
289D SER* 4.1 12.6 - - - -
320D SER* 2.7 45.3 + - - +
323D THR* 3.7 7.3 - - - +
324D LEU* 4.8 9.4 - - + +
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Residues in contact with ALA 283 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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280D LYS 4.0 3.4 + - - -
281D SER 3.2 0.2 - - - -
282D LEU* 1.3 77.9 - - - +
284D SER* 1.3 66.4 + - - +
285D GLY 3.2 1.3 - - - -
286D MET* 3.0 47.3 + - + +
288D LEU* 4.0 15.8 + - + -
316D CYS 3.7 22.7 - - - +
319D ALA* 4.0 3.5 - - - +
320D SER* 3.9 8.7 - - - +
323D THR* 3.9 2.2 - - - -
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Residues in contact with SER 284 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78C ILE* 3.8 20.8 - - - +
79C HIS* 3.9 0.3 - - - +
56D ALA 3.4 8.1 - - - -
57D ILE* 2.7 34.4 - - - +
58D ASN 6.0 0.2 - - - +
59D VAL* 3.3 23.8 - - - +
60D GLY 5.5 3.1 - - - -
66D VAL* 3.9 17.3 - - - +
281D SER 3.4 9.5 + - - -
283D ALA* 1.3 78.3 - - - +
285D GLY* 1.3 52.7 + - - +
286D MET 3.3 1.1 - - - -
323D THR* 2.7 24.8 + - - +
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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