Contacts of the helix formed by residues 284 - 290 (chain B) in PDB entry 4CDC
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 284 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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279B PRO 3.4 1.2 + - - -
280B TYR* 3.3 13.6 + - - +
282B ILE 3.1 1.0 - - - -
283B ALA* 1.3 81.8 - - - +
285B LYS* 1.3 58.4 + - - +
286B TYR 3.5 0.7 - - - -
287B ALA* 3.5 0.5 + - - +
288B GLN* 3.0 29.6 + - - +
318B SER* 4.1 1.3 - - - -
321B TYR* 3.3 34.4 - - - -
431C VAL* 5.4 1.0 - - - +
433C ALA* 4.3 0.6 - - - +
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Residues in contact with LYS 285 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A GLU* 2.8 27.1 + - - +
76A LYS* 4.1 9.3 + - - +
78A PHE* 3.5 38.2 - - + +
101A TRP* 5.2 2.7 - - - -
103A HIS* 3.4 28.2 + - - -
270B TYR* 3.9 14.6 - - + -
280B TYR 3.1 9.8 + - - +
281B LEU* 3.6 25.9 + - + +
284B GLY* 1.3 70.2 - - - +
286B TYR* 1.3 60.6 + - - +
288B GLN* 3.3 0.7 + - - -
289B ASP* 2.9 48.6 + - - +
321B TYR* 3.4 23.5 + - + +
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Residues in contact with TYR 286 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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263B GLU* 2.4 46.0 + - - -
264B VAL* 4.0 13.2 - - + -
267B CYS* 3.8 12.3 + - - +
268B SER* 3.2 27.6 - - - -
269B GLN* 3.6 19.1 - - - -
270B TYR* 3.7 12.3 - + + -
281B LEU 2.8 22.1 + - - +
282B ILE* 3.6 12.3 + - + +
284B GLY 3.5 0.2 - - - -
285B LYS* 1.3 69.4 - - - +
287B ALA* 1.3 61.1 + - - +
290B PHE* 2.8 57.6 + + + +
291B GLY 3.1 13.8 + - - -
292B LEU* 3.8 16.8 - - + -
315B ARG* 3.7 3.2 + - - -
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Residues in contact with ALA 287 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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243B LEU* 4.2 1.3 - - + -
282B ILE 3.0 10.9 + - - +
283B ALA 3.1 27.6 - - - +
285B LYS 3.4 0.2 - - - -
286B TYR* 1.3 77.3 - - - +
288B GLN* 1.3 60.2 + - - +
291B GLY* 3.2 10.6 + - - +
292B LEU* 3.9 23.1 - - + -
316B TYR 4.9 0.2 - - - +
317B TYR* 3.1 30.6 - - - -
318B SER* 3.4 16.2 - - - +
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Residues in contact with GLN 288 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76A LYS* 3.0 32.7 + - - +
103A HIS* 5.1 1.4 - - - -
105A VAL 4.3 8.2 - - - +
284B GLY 3.0 17.0 + - - +
285B LYS 3.9 3.4 - - - +
286B TYR 3.1 0.2 - - - -
287B ALA* 1.3 78.3 - - - +
289B ASP* 1.3 69.8 + - - +
317B TYR* 3.3 12.6 - - - -
318B SER 3.3 28.5 + - - +
319B SER* 3.4 21.8 + - - +
320B GLU* 4.3 0.6 - - - +
321B TYR* 3.6 20.2 + - + -
106D LEU* 4.4 18.2 - - + +
108D ARG* 3.1 23.0 + - - +
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Residues in contact with ASP 289 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A ARG* 3.2 27.6 + - - -
103A HIS* 3.1 33.8 + - - -
110A TRP* 3.7 13.7 - - + -
270B TYR* 2.7 23.8 + - - +
285B LYS* 2.9 27.9 + - - +
288B GLN* 1.3 90.5 - - - +
290B PHE* 1.3 76.4 + - + +
108D ARG* 4.1 11.4 + - - +
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Residues in contact with PHE 290 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A ARG* 3.2 58.9 + - + +
27A ASP* 5.1 1.6 - - - -
101A TRP* 5.8 1.6 - + - -
110A TRP* 3.7 14.6 - + - -
269B GLN* 3.7 26.0 - - + -
270B TYR* 3.5 26.0 - + - -
286B TYR* 2.8 51.5 + + + +
289B ASP* 1.3 80.1 - - + +
291B GLY* 1.3 58.1 + - - +
315B ARG* 2.8 28.2 + - - +
317B TYR* 3.5 7.1 - - - -
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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