Contacts of the helix formed by residues 303 - 317 (chain B) in PDB entry 1UES
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 303 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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297B ILE* 4.1 4.1 - - - +
298B ASP* 3.5 13.6 + - - +
301B PHE* 3.3 3.9 + - - +
302B GLY* 1.3 79.3 - - - +
304B PHE* 1.3 58.1 + - - +
305B GLU* 3.5 8.3 + - - +
306B LYS* 3.0 24.3 + - - +
307B PHE* 2.9 27.9 + - - +
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Residues in contact with PHE 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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287B GLY 3.4 23.6 - - - -
288B ALA* 3.8 18.2 - - + -
289B PRO* 3.4 32.3 - - + -
297B ILE* 4.0 11.7 - - + -
298B ASP* 3.4 9.9 + - - +
303B SER* 1.3 71.0 - - - +
305B GLU* 1.3 69.1 + - - +
307B PHE* 3.2 11.5 + + - +
308B LYS* 2.9 77.3 + - + +
379B TRP* 4.6 2.5 - + + -
384B TRP* 3.4 27.8 - + - -
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Residues in contact with GLU 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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303B SER* 3.2 8.1 + - - +
304B PHE* 1.3 86.1 - - - +
306B LYS* 1.3 62.0 + - - +
308B LYS* 3.2 31.2 + - + +
309B GLU* 3.0 22.2 + - - +
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Residues in contact with LYS 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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301B PHE 3.3 24.9 - - - +
302B GLY* 5.6 0.9 - - - -
303B SER* 3.0 20.1 + - - +
305B GLU* 1.3 74.5 - - - +
307B PHE* 1.3 57.6 + - - +
309B GLU* 3.1 19.7 + - - +
310B GLU* 2.7 59.9 + - - +
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Residues in contact with PHE 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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297B ILE* 3.7 20.6 - - + -
301B PHE* 3.9 31.8 - + + +
303B SER 2.9 14.3 + - - +
304B PHE* 3.2 22.2 + + - +
306B LYS* 1.3 75.7 - - - +
308B LYS* 1.3 54.3 + - - +
310B GLU* 3.0 11.2 + - - +
311B PHE* 2.7 64.8 + + - +
326B LEU* 3.9 36.8 - - + -
336B ILE* 4.1 5.2 - - + -
354B LEU* 4.4 2.9 - - + -
379B TRP* 3.6 26.9 - + - -
384B TRP* 4.3 11.9 - + - -
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Residues in contact with LYS 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 PHE* 2.9 66.9 + - + +
305B GLU* 3.2 29.4 + - + +
307B PHE* 1.3 75.7 - - + +
309B GLU* 1.3 54.2 + - - +
311B PHE* 3.6 0.5 - - - +
312B ASN* 2.7 43.1 + - - +
379B TRP* 3.9 52.3 - - + +
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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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305B GLU 3.0 14.2 + - - +
306B LYS* 3.4 22.3 + - - +
308B LYS* 1.3 76.0 - - - +
310B GLU* 1.3 75.7 + - - +
312B ASN* 3.4 7.3 + - - +
313B THR* 3.0 33.6 + - - +
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Residues in contact with GLU 310 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301B PHE* 4.2 15.3 - - + +
306B LYS* 2.7 54.5 + - - +
307B PHE* 3.4 10.3 - - - +
309B GLU* 1.3 91.7 - - - +
311B PHE* 1.3 62.1 + - - +
313B THR* 3.3 7.2 + - - -
314B ALA* 3.0 23.0 + - - +
336B ILE* 3.6 17.2 - - + +
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Residues in contact with PHE 311 (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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307B PHE* 2.7 34.4 + + + +
308B LYS 3.6 3.6 - - - +
310B GLU* 1.3 71.0 - - - +
312B ASN* 1.3 66.5 + - - +
314B ALA* 3.1 4.0 + - - +
315B GLY* 3.0 18.2 + - - -
324B VAL* 3.6 36.2 - - + +
325B TRP 3.6 7.2 - - - -
326B LEU* 3.5 27.8 - - + -
336B ILE* 3.7 13.9 - - + +
354B LEU* 3.8 26.2 - - + -
356B PHE* 3.7 35.7 - + - -
375B LEU* 5.0 0.2 - - - +
379B TRP* 3.5 29.4 - + + -
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Residues in contact with ASN 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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308B LYS* 2.7 26.1 + - - +
309B GLU* 3.7 7.1 - - - +
311B PHE* 1.3 73.5 - - - +
313B THR* 1.3 59.0 + - - +
315B GLY* 3.1 2.4 + - - -
316B THR* 2.9 35.0 + - - +
356B PHE* 4.2 2.0 - - - -
372B ALA 5.7 0.7 - - - +
375B LEU* 3.6 30.2 + - + +
376B LYS* 4.2 19.2 - - + +
379B TRP* 2.9 36.9 + - - +
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Residues in contact with THR 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* 3.0 25.8 + - - +
310B GLU* 3.6 6.7 - - - -
311B PHE 3.2 0.2 - - - -
312B ASN* 1.3 76.2 - - - +
314B ALA* 1.3 60.0 + - - +
316B THR* 4.4 5.4 - - - +
317B THR* 2.8 48.8 + - + +
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Residues in contact with ALA 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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310B GLU 3.0 10.2 + - - +
311B PHE 3.1 8.0 + - - +
313B THR* 1.3 77.0 - - - +
315B GLY* 1.3 62.7 + - - +
317B THR* 3.5 6.8 + - - -
318B LEU* 3.3 23.9 + - - +
324B VAL* 3.8 8.7 - - + -
336B ILE* 3.6 28.9 - - + -
338B LYS* 3.6 22.7 - - + +
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Residues in contact with GLY 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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311B PHE 3.0 11.2 + - - -
312B ASN 3.6 3.1 - - - -
314B ALA* 1.3 78.4 - - - +
316B THR* 1.3 57.9 + - - +
318B LEU* 3.4 8.5 + - - +
324B VAL* 3.9 20.1 - - - +
358B VAL* 3.9 6.3 - - - +
371B ARG* 3.0 26.0 + - - -
375B LEU* 3.6 18.2 - - - -
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Residues in contact with THR 316 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312B ASN* 2.9 18.4 + - - +
313B THR* 3.3 6.5 + - - -
315B GLY* 1.3 76.6 - - - +
317B THR* 1.3 64.2 + - + +
318B LEU 3.6 0.7 + - - +
371B ARG* 3.9 18.5 + - + +
372B ALA* 3.7 35.7 - - + +
375B LEU* 3.6 4.2 - - - +
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Residues in contact with THR 317 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313B THR* 2.8 40.9 + - + +
314B ALA* 3.5 1.0 + - - -
316B THR* 1.3 81.3 - - + +
318B LEU* 1.3 62.7 + - - +
319B PHE* 3.2 6.8 + - - +
338B LYS* 2.8 35.9 + - - -
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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