Contacts of the helix formed by residues 298 - 310 (chain B) in PDB entry 1USK
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 GLU 298 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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296B SER* 3.1 15.4 + - - +
297B ASP* 1.3 85.2 - - - +
299B PRO* 1.3 71.7 - - + +
300B LEU* 4.6 2.5 - - + +
301B ALA* 3.2 26.7 + - + +
302B LEU* 3.2 16.6 + - - +
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Residues in contact with PRO 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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71B LYS* 3.9 31.4 - - + +
72B TYR* 4.4 1.6 - - + -
93B GLY 3.1 30.1 - - - +
95B LEU* 3.6 23.4 - - + +
113B HIS* 4.4 3.6 - - + +
297B ASP 3.3 10.3 - - - +
298B GLU* 1.3 83.3 - - + +
300B LEU* 1.3 61.4 + - - +
302B LEU* 3.3 10.5 + - + -
303B VAL* 3.3 27.8 + - - +
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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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112B GLN* 3.8 44.2 - - + +
113B HIS* 4.1 24.5 + - + +
298B GLU* 3.3 3.4 - - + +
299B PRO* 1.3 78.8 - - - +
301B ALA* 1.3 62.4 + - - +
303B VAL* 3.5 3.0 + - + +
304B LYS* 3.2 25.7 + - + +
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Residues in contact with ALA 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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294B THR* 4.4 4.8 - - + +
296B SER* 3.8 15.5 - - - +
298B GLU* 3.2 33.4 + - + +
300B LEU* 1.3 78.9 - - - +
302B LEU* 1.3 57.8 + - - +
304B LYS* 3.9 10.3 - - - +
305B ASP* 3.2 26.0 + - - +
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Residues in contact with LEU 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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72B TYR* 3.4 35.9 - - + -
95B LEU* 3.7 13.9 - - + -
287B LEU* 4.5 2.5 - - + -
290B ALA* 3.3 44.6 - - + +
291B LEU* 3.6 20.6 - - + +
294B THR* 3.5 12.1 - - - +
296B SER* 4.0 10.5 - - - +
298B GLU 3.2 17.6 + - - +
299B PRO 3.6 5.4 - - - +
300B LEU 3.2 0.4 - - - -
301B ALA* 1.3 76.3 - - - +
303B VAL* 1.3 65.4 + - - +
304B LYS 3.3 0.2 - - - -
305B ASP* 3.3 4.6 + - - +
306B LEU* 3.1 27.8 + - - +
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Residues in contact with VAL 303 (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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95B LEU* 3.7 19.3 - - + -
112B GLN 3.4 24.7 - - - +
113B HIS* 3.9 22.2 - - - +
114B ILE 4.8 0.2 - - - +
115B MET* 3.9 26.0 - - + -
299B PRO 3.3 14.0 + - - +
300B LEU* 3.5 6.5 + - + +
302B LEU* 1.3 75.6 - - - +
304B LYS* 1.3 63.0 + - - +
306B LEU* 3.4 2.8 + - - +
307B LYS* 3.1 48.0 + - + +
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Residues in contact with LYS 304 (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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300B LEU* 3.2 20.0 + - + +
301B ALA* 3.9 10.1 - - - +
303B VAL* 1.3 82.1 - - - +
305B ASP* 1.3 63.6 + - + +
307B LYS* 3.6 9.8 + - - +
308B ALA* 3.2 34.3 + - - +
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Residues in contact with ASP 305 (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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290B ALA* 3.5 17.8 - - - +
293B ARG* 3.1 34.0 + - - +
294B THR* 3.3 33.4 - - + +
301B ALA 3.2 12.8 + - - +
302B LEU* 3.6 6.1 - - - +
303B VAL 3.2 0.4 - - - -
304B LYS* 1.3 81.2 - - + +
306B LEU* 1.3 60.3 + - - +
308B ALA* 3.5 1.1 + - - -
309B ASN* 3.1 49.6 + - - +
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Residues in contact with LEU 306 (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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95B LEU* 5.7 2.9 - - + -
97B ILE* 4.3 9.4 - - + -
115B MET* 3.7 35.9 - - + -
286B SER* 3.4 41.7 - - - +
287B LEU* 4.6 1.3 - - - +
289B THR* 4.7 0.2 - - - -
290B ALA* 3.9 14.4 - - + +
293B ARG* 4.3 5.2 - - - +
302B LEU 3.1 18.9 + - - +
303B VAL* 3.4 1.3 + - - +
305B ASP* 1.3 73.6 - - - +
307B LYS* 1.3 63.0 + - - +
310B GLY* 2.9 44.3 + - - +
311B ALA* 4.3 4.7 - - + -
320B TRP* 3.4 21.4 + - + +
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Residues in contact with LYS 307 (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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111B TYR 4.6 7.7 + - - -
112B GLN* 4.1 15.4 + - - +
114B ILE 4.7 1.8 + - - -
115B MET* 4.6 3.4 - - + -
303B VAL* 3.1 40.5 + - + +
304B LYS* 3.9 7.9 - - - +
305B ASP 3.4 0.2 - - - -
306B LEU* 1.3 75.2 - - - +
308B ALA* 1.3 60.8 + - - +
310B GLY 5.1 0.2 + - - -
319B ASN* 4.7 5.2 - - - +
320B TRP* 3.5 28.7 - - + +
321B ASP 3.7 19.7 - - - +
322B GLU* 3.0 35.0 + - + +
323B LYS 4.5 1.8 - - - -
324B GLY* 3.9 14.2 - - - +
327B LYS* 5.8 0.2 + - - -
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Residues in contact with ALA 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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304B LYS* 3.2 28.4 + - - +
305B ASP* 3.5 1.1 + - - -
307B LYS* 1.3 79.8 - - - +
309B ASN* 1.3 76.5 + - - +
310B GLY 3.9 0.2 - - - -
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Residues in contact with ASN 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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293B ARG* 3.7 28.0 + - - +
305B ASP* 3.1 35.8 + - - +
308B ALA* 1.3 91.6 - - - +
310B GLY* 1.3 63.4 + - - +
311B ALA 4.0 0.2 + - - -
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Residues in contact with GLY 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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293B ARG* 2.8 26.3 + - - -
305B ASP 4.1 0.2 + - - -
306B LEU* 2.9 21.5 + - - +
307B LYS 5.1 0.2 + - - -
308B ALA 3.9 0.4 - - - -
309B ASN* 1.3 78.5 - - - +
311B ALA* 1.3 63.0 + - - +
318B LEU 3.2 17.0 - - - -
319B ASN* 4.9 5.1 + - - -
320B TRP* 3.8 6.7 - - - -
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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