Contacts of the helix formed by residues 307 - 319 (chain B) in PDB entry 3KSA
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 ASN 307 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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282B ALA* 4.7 18.6 - - + -
283B GLY* 5.2 2.9 - - - +
305B ASP* 2.6 19.4 + - + +
306B ALA* 1.3 67.9 - - - +
308B THR* 1.3 63.5 + - - +
309B GLU 3.2 2.7 - - - -
310B LEU* 2.9 19.1 + - + +
311B VAL* 2.9 20.6 + - + +
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Residues in contact with THR 308 (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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253B GLN 6.3 1.8 - - - +
254B ILE* 4.9 5.9 - - - +
302B LEU* 3.8 30.5 - - + +
306B ALA* 2.5 49.4 + - + +
307B ASN* 1.3 68.8 - - - +
309B GLU* 1.3 62.6 + - - +
311B VAL* 3.0 3.8 + - - +
312B LEU* 2.7 37.5 + - - +
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Residues in contact with GLU 309 (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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306B ALA 4.7 0.2 + - - -
307B ASN 3.2 1.0 - - - -
308B THR* 1.3 86.9 + - - +
310B LEU* 1.3 58.2 + - - +
312B LEU* 3.9 15.7 - - - +
313B ASN* 2.9 34.1 + - - +
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Residues in contact with LEU 310 (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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281B VAL* 5.0 4.6 - - + +
282B ALA* 6.4 0.9 - - + -
307B ASN* 2.9 20.7 + - + +
309B GLU* 1.3 77.8 - - - +
311B VAL* 1.3 57.6 + - - +
313B ASN* 4.0 4.3 - - - +
314B TYR* 2.9 31.0 + - - +
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Residues in contact with VAL 311 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254B ILE* 5.3 2.5 - - + -
281B VAL* 4.7 19.4 - - + +
282B ALA* 6.3 0.4 - - + -
283B GLY* 5.3 8.3 - - - +
284B ILE* 5.4 2.9 - - - +
302B LEU* 4.5 16.6 - - + -
307B ASN* 2.9 12.9 + - + +
308B THR* 3.0 12.8 + - - +
310B LEU* 1.3 74.5 - - - +
312B LEU* 1.3 58.4 + - - +
314B TYR* 3.3 7.2 + - - +
315B LEU* 2.9 36.6 + - + +
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Residues in contact with LEU 312 (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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242B THR* 4.5 19.3 - - - -
254B ILE* 4.5 27.3 - - + +
308B THR 2.7 20.4 + - - +
309B GLU* 3.9 17.3 - - - +
311B VAL* 1.3 69.9 - - - +
313B ASN* 1.3 66.3 + - - +
315B LEU* 3.1 10.0 + - + +
316B PHE* 2.9 60.8 + - + +
321B LEU* 5.3 4.7 - - + -
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Residues in contact with ASN 313 (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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309B GLU* 2.9 21.7 + - - +
310B LEU* 4.0 4.9 - - - +
312B LEU* 1.3 76.1 - - - +
314B TYR* 1.3 63.2 + - - +
316B PHE* 3.6 12.2 + - - +
317B LYS* 3.4 18.0 + - - +
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Residues in contact with TYR 314 (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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275B VAL* 3.9 22.5 - - + +
280B LYS* 3.6 25.7 + - + +
281B VAL* 3.7 37.7 - - + -
310B LEU 2.9 20.0 + - - +
311B VAL 3.5 4.3 - - - +
313B ASN* 1.3 74.3 - - - +
315B LEU* 1.3 73.5 + - + +
317B LYS* 2.9 9.5 + - + +
318B TYR* 2.8 50.8 + - + +
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Residues in contact with LEU 315 (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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254B ILE* 5.2 4.7 - - + -
272B ILE* 4.1 22.0 - - + -
275B VAL* 4.5 21.3 - - + -
281B VAL* 6.4 0.7 - - + -
300B ILE* 3.3 37.9 - - + -
311B VAL* 2.9 22.8 + - + +
312B LEU* 3.1 14.3 + - + +
314B TYR* 1.3 76.5 - - + +
316B PHE* 1.3 63.7 + - - +
319B THR* 2.8 52.8 + - + +
321B LEU* 4.3 15.7 - - + +
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Residues in contact with PHE 316 (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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239B ARG* 4.5 10.5 - - + -
240B SER* 3.8 33.7 - - - -
242B THR* 5.2 6.1 - - - -
312B LEU* 2.9 45.2 + - + -
313B ASN* 3.7 13.9 - - - +
315B LEU* 1.3 76.3 - - - +
317B LYS* 1.3 63.6 + - - +
319B THR 3.0 15.2 - - - +
321B LEU* 3.9 15.7 - - + -
322B GLN* 3.4 36.8 - - + +
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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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313B ASN 3.4 9.4 + - - +
314B TYR* 2.9 12.7 + - + +
316B PHE* 1.3 84.1 - - - +
318B TYR* 1.3 61.7 + - + +
319B THR 3.4 3.1 + - - +
322B GLN 5.1 0.3 - - - +
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Residues in contact with TYR 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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275B VAL* 5.2 2.2 - - + -
314B TYR* 2.8 58.2 + - + +
317B LYS* 1.3 74.1 - - + +
319B THR* 1.3 64.2 + - + +
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Residues in contact with THR 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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268B LEU* 4.3 7.8 - - - +
271B LYS* 4.3 26.2 - - + +
272B ILE* 4.4 8.1 - - + +
275B VAL* 4.4 9.2 - - + -
315B LEU* 2.8 44.5 + - + +
316B PHE 3.0 18.9 - - - +
317B LYS 3.8 2.8 - - - +
318B TYR* 1.3 80.0 - - + +
320B ASP* 1.3 61.0 + - - +
321B LEU* 3.1 20.9 + - - +
322B GLN 3.3 5.7 - - - +
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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