Contacts of the helix formed by residues 302 - 314 (chain C) in PDB entry 4U8T
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 PRO 302 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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215A GLU* 3.5 32.8 - - + +
244A ASN* 5.4 2.9 - - - +
284C ILE* 4.3 11.4 - - + -
285C PRO* 4.3 14.1 - - + -
286C ALA* 6.1 0.7 - - + +
300C GLU 4.2 4.3 - - - +
301C ILE* 1.3 92.5 - - + +
303C ALA* 1.3 61.2 + - - +
304C THR* 3.4 6.5 - - + -
305C ILE* 3.5 27.6 + - + -
306C SER* 2.8 30.4 + - - -
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Residues in contact with ALA 303 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215A GLU* 3.2 14.3 + - - +
178C SER 4.8 6.1 - - - +
180C PHE* 3.9 24.3 - - + -
301C ILE 3.8 0.8 + - - -
302C PRO* 1.3 72.1 - - - +
304C THR* 1.3 63.7 + - - +
306C SER* 3.1 1.9 + - - -
307C LYS* 3.0 37.8 + - - +
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Residues in contact with THR 304 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215A GLU* 4.6 8.2 + - - +
302C PRO* 4.6 9.6 - - + -
303C ALA* 1.3 79.9 - - - +
305C ILE* 1.3 78.4 + - + +
307C LYS* 3.5 8.2 + - - +
308C SER* 3.3 22.3 + - - -
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Residues in contact with ILE 305 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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282C PHE* 3.9 31.2 - - + -
283C LEU 3.3 27.6 - - - +
284C ILE* 4.7 3.4 - - + -
285C PRO* 4.2 6.7 - - + -
301C ILE* 3.7 17.0 - - + -
302C PRO* 3.5 30.0 + - + +
304C THR* 1.3 81.1 - - + +
306C SER* 1.3 66.7 + - - +
308C SER* 3.1 10.6 + - - -
309C ILE* 3.1 23.0 + - + +
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Residues in contact with SER 306 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180C PHE* 3.2 47.3 - - - +
226C LEU* 5.4 4.3 - - - +
301C ILE* 3.2 16.5 - - - +
302C PRO 2.8 23.1 + - - -
303C ALA 3.1 4.9 + - - -
305C ILE* 1.3 77.0 - - - +
307C LYS* 1.3 57.6 + - - +
309C ILE* 3.0 10.6 + - - +
310C LEU* 2.8 31.8 + - - +
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Residues in contact with LYS 307 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174C VAL* 3.9 44.2 + - + +
176C ASP* 4.6 14.6 + - - +
180C PHE* 4.9 6.3 - - + -
303C ALA* 3.0 26.2 + - - +
304C THR* 3.9 6.3 - - - +
306C SER* 1.3 72.9 - - - +
308C SER* 1.3 65.5 + - - +
310C LEU* 3.9 9.0 - - + +
311C LYS* 3.2 27.2 + - - +
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Residues in contact with SER 308 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282C PHE* 3.5 23.7 - - - -
304C THR* 3.3 11.8 + - - -
305C ILE* 3.1 12.2 + - - -
307C LYS* 1.3 76.6 - - - +
309C ILE* 1.3 63.6 + - - +
311C LYS* 3.2 31.5 + - - +
312C LEU* 3.2 21.5 - - - +
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Residues in contact with ILE 309 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226C LEU* 4.1 20.0 - - + -
235C PHE* 6.3 0.7 - - + -
279C LEU* 3.8 17.0 - - + -
282C PHE* 3.6 28.5 - - + -
292C VAL* 3.9 31.6 - - + -
301C ILE* 4.6 4.5 - - + -
305C ILE* 3.1 21.6 + - + +
306C SER* 3.0 9.5 + - - +
308C SER* 1.3 75.4 - - - +
310C LEU* 1.3 65.1 + - - +
312C LEU* 3.0 21.0 + - - +
313C PHE* 3.3 30.9 + - + -
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Residues in contact with LEU 310 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172C ILE* 4.4 29.8 - - + +
174C VAL* 4.0 26.2 - - + -
180C PHE* 4.3 17.7 - - + -
224C TYR* 5.0 5.2 - - + -
226C LEU* 4.3 13.5 - - + -
238C VAL* 4.0 33.2 - - + -
306C SER* 2.8 18.1 + - - +
307C LYS* 3.9 10.8 - - + +
308C SER 3.3 0.2 - - - -
309C ILE* 1.3 77.3 - - + +
311C LYS* 1.3 63.1 + - - +
313C PHE* 3.2 17.6 + - + +
314C LYS* 3.5 12.1 + - - +
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Residues in contact with LYS 311 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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307C LYS 3.2 14.8 + - - +
308C SER* 3.4 35.0 + - - +
309C ILE 3.1 0.6 - - - -
310C LEU* 1.3 77.2 - - - +
312C LEU* 1.3 65.7 + - + +
314C LYS* 3.1 22.0 + - - +
315C TYR* 4.0 3.3 + - - +
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Residues in contact with LEU 312 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272C ARG* 3.7 13.9 + - - -
274C VAL* 3.9 19.9 - - + +
278C SER* 3.3 39.5 - - - +
279C LEU* 4.1 12.8 - - + -
281C GLN* 5.8 0.9 - - - +
282C PHE* 4.3 13.5 - - + -
308C SER* 3.2 26.5 - - - +
309C ILE* 3.0 10.7 + - - +
311C LYS* 1.3 82.5 - - + +
313C PHE* 1.3 61.4 + - + +
314C LYS 3.3 0.5 + - - -
315C TYR* 3.7 10.2 + - - +
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Residues in contact with PHE 313 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168C ILE* 4.1 5.4 - - - +
172C ILE* 5.8 0.9 - - + -
226C LEU* 4.9 7.2 - - + -
235C PHE* 3.6 30.7 - + + -
237C GLY* 3.7 24.0 - - - -
238C VAL* 4.1 17.5 - - + -
270C VAL* 3.8 38.5 - - + +
272C ARG* 3.3 42.6 + - + -
274C VAL* 3.8 22.0 - - + -
279C LEU* 5.5 1.8 - - + -
309C ILE* 3.3 38.0 + - + -
310C LEU* 3.2 14.5 + - + +
312C LEU* 1.3 78.6 - - + +
314C LYS* 1.3 58.0 + - + +
315C TYR 3.4 1.1 - - - -
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Residues in contact with LYS 314 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168C ILE* 3.4 20.0 - - + -
169C PRO* 2.7 25.7 + - + +
170C PRO* 2.3 39.6 + - - +
171C TRP* 5.8 2.5 - - - -
172C ILE* 5.3 11.0 - - + -
272C ARG* 3.9 0.2 - - - -
310C LEU 3.5 8.3 + - - +
311C LYS* 3.1 14.3 + - - +
312C LEU 3.1 1.0 - - - -
313C PHE* 1.3 78.1 - - - +
315C TYR* 1.3 59.0 + - - +
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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