Contacts of the helix formed by residues 316 - 325 (chain B) in PDB entry 1KWS
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 MET 316 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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220A LEU* 4.9 1.6 - - - -
223A GLY 3.5 5.8 - - - +
224A LEU 4.0 15.5 - - - +
225A ARG* 3.4 42.8 - - + +
87B LEU* 3.6 37.5 - - + -
314B PRO* 3.6 11.6 + - - +
315B LYS* 1.3 81.6 - - - +
317B LYS* 1.3 64.9 + - - +
318B GLN 3.3 2.2 - - - -
319B GLU* 3.2 16.1 + - + -
320B GLU* 3.2 36.6 + - + +
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Residues in contact with LYS 317 (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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223A GLY 4.1 0.2 + - - -
315B LYS* 3.7 5.9 - - + +
316B MET* 1.3 76.3 - - - +
318B GLN* 1.3 78.9 + - - +
320B GLU* 3.3 14.8 + - - +
321B GLN* 3.1 34.9 + - - +
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Residues in contact with GLN 318 (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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222A GLY 3.5 18.4 - - - +
223A GLY* 3.2 25.0 + - - +
224A LEU* 3.7 10.8 - - + -
242A ALA* 3.7 19.2 - - + +
243A TRP* 4.3 16.2 - - + +
315B LYS* 5.5 2.1 - - - +
316B MET 3.3 0.4 - - - -
317B LYS* 1.3 88.6 + - - +
319B GLU* 1.3 57.5 + - - +
321B GLN* 3.2 22.5 + - - +
322B LEU* 2.9 32.4 + - - +
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Residues in contact with GLU 319 (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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223A GLY 3.0 13.2 + - - +
224A LEU* 3.5 10.8 - - - +
225A ARG* 2.8 25.8 + - + +
316B MET* 3.2 32.0 + - + +
318B GLN* 1.3 77.0 - - - +
320B GLU* 1.3 53.5 + - + +
322B LEU* 3.2 3.9 + - - +
323B GLN* 2.7 60.9 + - + +
328B GLY* 3.4 5.3 - - - -
329B SER* 2.6 49.0 + - - +
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Residues in contact with GLU 320 (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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316B MET* 3.2 26.8 + - + +
317B LYS* 3.3 10.8 + - - +
319B GLU* 1.3 77.5 - - + +
321B GLN* 1.3 62.6 + - + +
323B GLN* 3.2 11.5 + - + +
324B ARG* 3.0 30.2 + - + +
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Residues in contact with GLN 321 (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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242A ALA* 5.5 3.1 - - + +
317B LYS* 3.1 32.9 + - - +
318B GLN* 3.4 25.5 + - - +
319B GLU 3.2 0.2 - - - -
320B GLU* 1.3 75.3 - - + +
322B LEU* 1.3 66.3 + - + +
324B ARG* 3.2 24.3 + - - +
325B GLN* 3.3 22.5 + - - +
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Residues in contact with LEU 322 (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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224A LEU* 3.6 27.6 - - + -
240A HIS* 3.6 26.5 - - + +
241A THR 4.3 12.1 - - - +
242A ALA* 4.3 12.6 - - + -
318B GLN 2.9 17.6 + - - +
319B GLU* 3.7 4.7 - - - +
321B GLN* 1.3 75.8 - - + +
323B GLN* 1.3 59.5 + - - +
325B GLN* 3.1 10.7 + - - +
326B GLY 3.1 3.6 + - - -
327B ARG* 2.7 76.8 + - + +
328B GLY* 3.8 4.5 - - - +
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Residues in contact with GLN 323 (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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225A ARG* 5.4 3.1 - - - -
319B GLU* 2.7 58.1 + - + +
320B GLU* 3.2 12.3 - - + +
322B LEU* 1.3 73.8 - - - +
324B ARG* 1.3 56.4 + - + +
326B GLY* 2.7 24.5 + - - -
328B GLY* 4.0 13.0 - - - +
329B SER 4.7 2.4 + - - +
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Residues in contact with ARG 324 (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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320B GLU 3.0 15.6 + - - +
321B GLN* 3.4 14.8 - - - +
323B GLN* 1.3 79.3 - - + +
325B GLN* 1.3 62.3 + - + +
326B GLY 3.2 0.6 + - - -
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Residues in contact with GLN 325 (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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321B GLN* 3.3 19.8 + - - +
322B LEU* 3.1 14.4 + - - +
323B GLN 3.0 1.2 - - - -
324B ARG* 1.3 78.4 - - + +
326B GLY* 1.3 61.6 + - - +
327B ARG* 2.8 47.1 + - - +
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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