Contacts of the helix formed by residues 292 - 302 (chain B) in PDB entry 3K5N
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 SER 292 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223B TRP* 3.6 4.3 - - - +
290B SER* 3.6 7.6 + - - -
291B PHE* 1.3 78.7 - - - +
293B LEU* 1.3 67.5 + - - +
294B GLU* 2.3 32.7 + - - -
295B THR* 3.2 17.5 + - - -
296B VAL* 2.5 20.2 + - - +
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Residues in contact with LEU 293 (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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156B ASP* 5.1 3.6 - - - +
223B TRP* 3.2 40.3 - - + +
292B SER* 1.3 73.6 - - - +
294B GLU* 1.3 64.8 + - + +
296B VAL* 2.9 3.2 + - - +
297B ALA* 2.6 39.6 + - + +
335B ASN* 4.0 37.0 - - + +
338B LEU* 3.9 22.9 - - + -
339B VAL* 3.7 27.1 - - + +
342B ILE* 4.5 8.9 - - + +
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Residues in contact with GLU 294 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292B SER* 2.3 35.6 + - - -
293B LEU* 1.3 85.5 + - + +
295B THR* 1.3 60.3 + - - +
297B ALA* 3.8 4.3 - - - +
298B GLN* 3.0 33.8 + - + +
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Residues in contact with THR 295 (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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289B SER* 3.7 5.8 - - - +
290B SER* 3.5 39.9 - - - +
292B SER* 3.0 13.0 + - - -
294B GLU* 1.3 79.7 + - - +
296B VAL* 1.3 59.0 + - - +
298B GLN* 3.5 13.9 + - - +
299B GLU* 2.8 56.8 + - + +
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Residues in contact with VAL 296 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223B TRP* 3.6 31.4 - - + -
281B LEU* 4.5 2.2 - - + -
288B PHE* 4.0 35.2 - - + -
290B SER 3.9 3.1 - - - +
291B PHE* 3.7 11.9 - - + -
292B SER 2.5 41.7 - - - +
293B LEU* 3.3 2.9 - - - +
295B THR* 1.3 79.2 - - - +
297B ALA* 1.3 57.4 + - - +
299B GLU* 3.5 0.9 + - - +
300B LEU* 2.9 32.2 + - + +
342B ILE* 4.3 10.5 - - + -
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Residues in contact with ALA 297 (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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293B LEU 2.6 22.2 + - - +
294B GLU* 3.8 5.8 - - - +
296B VAL* 1.3 71.1 - - - +
298B GLN* 1.3 67.0 + - - +
301B LEU* 2.8 40.0 + - + +
302B GLY 3.0 1.4 + - - -
303B GLU* 3.3 12.0 + - + -
338B LEU* 3.9 31.2 - - + -
342B ILE* 4.9 2.9 - - + -
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Residues in contact with GLN 298 (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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294B GLU* 3.0 26.9 + - + +
295B THR* 3.8 14.8 + - - +
296B VAL 3.4 0.2 - - - -
297B ALA* 1.3 74.7 - - + +
299B GLU* 1.3 63.4 + - + +
302B GLY* 2.7 30.6 + - - -
303B GLU* 3.7 26.0 + - - +
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Residues in contact with GLU 299 (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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287B ASN 5.4 0.5 - - - +
288B PHE* 3.9 21.8 - - + -
289B SER* 2.3 39.2 + - - -
295B THR* 2.8 30.3 + - + +
296B VAL 3.8 2.7 - - - +
298B GLN* 1.3 85.1 - - + +
300B LEU* 1.3 58.2 + - - +
302B GLY* 4.7 0.7 + - - -
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Residues in contact with LEU 300 (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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286B TRP* 4.0 27.1 - - + -
288B PHE* 3.9 19.3 - - + -
296B VAL* 2.9 18.2 + - + +
299B GLU* 1.3 75.4 - - - +
301B LEU* 1.3 65.2 + - + +
302B GLY 3.4 0.6 + - - -
342B ILE* 4.2 19.1 - - + -
345B LYS* 4.1 39.8 - - + +
346B THR* 3.5 29.8 - - + -
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Residues in contact with LEU 301 (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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297B ALA* 2.8 33.2 + - + +
300B LEU* 1.3 78.6 - - + +
302B GLY* 1.3 58.1 + - - +
303B GLU* 3.0 14.3 + - + +
338B LEU* 4.1 19.7 - - + +
341B GLN* 4.1 26.2 - - + +
342B ILE* 3.6 29.2 - - + +
345B LYS* 4.6 24.2 - - + -
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Residues in contact with GLY 302 (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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298B GLN* 2.7 25.4 + - - -
299B GLU 5.3 0.4 - - - -
300B LEU 3.4 1.8 - - - -
301B LEU* 1.3 73.7 - - - +
303B GLU* 1.3 68.6 + - - +
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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