Contacts of the helix formed by residues 295 - 311 (chain C) in PDB entry 4U1D
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 ASP 295 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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257C TYR* 4.9 1.7 - - - -
290C PHE* 3.2 17.8 + - + +
293C SER* 2.7 22.7 + - - +
294C GLY* 1.3 80.5 - - - +
296C PRO* 1.3 63.0 - - + +
297C LEU 3.4 2.0 - - - -
298C LEU* 3.3 32.1 + - + +
299C HIS* 3.0 21.8 + - - +
346C ASP* 4.7 4.9 - - - +
348C HIS* 2.9 33.0 + - - +
352C TYR* 5.6 3.4 + - - +
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Residues in contact with PRO 296 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290C PHE 5.1 0.4 - - - +
294C GLY 3.3 11.9 - - - +
295C ASP* 1.3 83.6 - - + +
297C LEU* 1.3 67.3 + - + +
299C HIS* 3.4 11.9 - - + +
300C THR* 2.9 31.9 + - - -
331C SER 4.8 2.5 - - - +
334C SER 5.7 0.2 - - - +
335C THR* 3.8 36.6 + - + +
336C GLN* 4.8 10.1 - - + +
352C TYR* 6.2 0.2 - - - +
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Residues in contact with LEU 297 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296C PRO* 1.3 79.4 - - + +
298C LEU* 1.3 65.3 + - - +
300C THR* 3.4 2.2 + - - +
301C THR* 3.1 26.5 + - - -
332C ALA* 6.3 0.2 - - - -
335C THR* 4.1 26.5 - - + +
338C ASP* 4.3 7.9 - - - +
352C TYR* 4.6 19.3 - - + +
361C PRO* 3.2 41.1 - - + +
362C THR 4.1 10.1 - - - +
363C ARG* 4.1 4.3 - - - -
366C MET* 3.5 38.1 - - + +
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Residues in contact with LEU 298 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290C PHE* 3.5 45.1 - - + -
295C ASP* 3.3 28.3 + - + +
296C PRO 3.3 0.4 - - - -
297C LEU* 1.3 76.0 - - - +
299C HIS* 1.3 58.4 + - - +
301C THR* 3.1 6.0 + - - -
302C ALA 2.9 26.5 + - - -
348C HIS 4.9 3.6 - - - +
351C MET* 3.7 29.6 - - + +
352C TYR* 3.8 37.0 - - + +
355C LEU* 3.8 19.6 - - + +
357C LEU* 5.1 4.0 - - + -
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Residues in contact with HIS 299 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287C VAL* 2.8 31.6 + - + +
290C PHE* 3.6 16.3 - - + +
291C PHE* 3.9 25.7 - + + +
295C ASP 3.0 14.1 + - - +
296C PRO* 3.4 14.4 - - + +
298C LEU* 1.3 77.4 - - - +
300C THR* 1.3 62.4 + - - +
302C ALA* 3.4 3.5 + - - +
303C TRP* 3.1 48.9 + + - -
331C SER* 4.0 16.4 - - - -
419C GLN* 5.5 1.8 - - - -
420C TYR* 2.6 32.5 + + - -
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Residues in contact with THR 300 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296C PRO 2.9 16.1 + - - -
297C LEU* 3.7 7.5 - - - +
298C LEU 3.3 0.2 - - - -
299C HIS* 1.3 75.8 - - - +
301C THR* 1.3 58.0 + - - +
303C TRP* 3.1 9.3 + - - +
304C LYS* 2.8 27.6 + - + +
328C ILE* 3.8 9.6 - - + +
331C SER* 3.1 33.7 + - - +
332C ALA* 4.3 3.6 + - + -
335C THR* 4.5 1.2 + - - -
366C MET* 3.6 28.0 - - + +
370C ILE* 3.7 22.2 - - + -
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Residues in contact with THR 301 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297C LEU 3.1 14.6 + - - -
298C LEU* 3.4 9.8 - - - -
300C THR* 1.3 74.3 - - - +
302C ALA* 1.3 60.9 + - - +
304C LYS* 3.0 11.5 + - - +
305C LYS* 2.8 44.0 + - + +
355C LEU* 3.6 21.1 - - + -
357C LEU* 4.1 30.2 - - + +
366C MET* 3.3 16.5 - - - +
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Residues in contact with ALA 302 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283C TYR* 3.8 8.5 - - - +
286C LEU* 3.6 30.1 - - + +
287C VAL* 3.6 22.7 - - + +
290C PHE* 4.3 3.4 - - + -
298C LEU 2.9 15.1 + - - +
299C HIS 3.8 2.5 - - - +
301C THR* 1.3 77.2 - - - +
303C TRP* 1.3 56.1 + - - +
305C LYS* 3.4 9.3 + - - +
306C PHE* 2.9 29.5 + - - +
355C LEU* 4.4 2.4 - - + +
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Residues in contact with TRP 303 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284C GLU* 6.4 2.2 - - + -
287C VAL* 3.5 25.0 - - + +
299C HIS* 3.1 50.6 + + - +
300C THR* 3.1 12.9 + - - +
302C ALA* 1.3 76.7 - - - +
304C LYS* 1.3 51.8 + - - +
306C PHE* 3.1 24.6 + + - +
307C TYR* 2.7 35.7 + - + +
324C TYR* 3.8 46.2 - + + -
327C THR* 3.6 28.6 - - + +
328C ILE* 3.7 28.2 - - + +
331C SER* 5.5 1.6 - - - -
419C GLN* 5.8 0.6 - - - +
420C TYR* 4.3 0.4 + - - -
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Residues in contact with LYS 304 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300C THR* 2.8 18.4 + - + +
301C THR* 3.0 10.2 + - - +
303C TRP* 1.3 72.0 - - - +
305C LYS* 1.3 57.8 + - + +
307C TYR* 3.1 2.6 + - - +
308C LYS* 2.8 33.7 + - - +
328C ILE* 3.9 21.8 - - + -
366C MET* 3.5 29.8 - - - +
369C SER* 2.7 36.7 + - - -
370C ILE* 4.0 13.7 - - + -
376C ILE* 4.1 17.5 - - + +
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Residues in contact with LYS 305 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283C TYR* 3.6 48.7 + - + -
301C THR* 2.8 32.4 + - + +
302C ALA* 3.7 6.3 - - - +
304C LYS* 1.3 75.5 - - - +
306C PHE* 1.3 60.0 + - - +
308C LYS* 3.8 8.6 + - + +
309C LEU* 3.4 22.2 + - - +
355C LEU* 3.2 35.7 + - + +
356C ASN* 4.2 15.6 - - - +
357C LEU* 5.0 2.0 - - - -
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Residues in contact with PHE 306 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280C ALA* 3.4 37.7 - - + -
283C TYR* 3.8 15.4 - - + +
284C GLU* 3.7 35.7 - - + -
287C VAL* 5.2 1.1 - - + -
302C ALA 2.9 18.1 + - - +
303C TRP* 3.4 28.0 - + + +
305C LYS* 1.3 75.7 - - - +
307C TYR* 1.3 64.0 + - - +
309C LEU* 3.3 3.3 + - - +
310C TYR* 2.9 46.6 + + + +
324C TYR* 3.6 38.4 - + - -
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Residues in contact with TYR 307 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303C TRP 2.7 19.5 + - - +
304C LYS* 3.6 4.3 - - - +
306C PHE* 1.3 78.0 - - + +
308C LYS* 1.3 65.7 + - - +
310C TYR* 3.2 3.8 + + - +
311C SER* 3.0 30.9 + - - -
321C PHE* 3.4 34.9 - + - -
324C TYR* 3.9 30.1 - + + -
325C SER* 2.9 29.5 + - - -
328C ILE* 3.6 17.9 - - + -
375C SER* 2.9 34.7 + - - -
376C ILE* 3.5 26.5 - - + -
379C LYS* 3.7 6.4 - - - +
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Residues in contact with LYS 308 (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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304C LYS 2.8 17.1 + - - +
305C LYS* 4.1 8.1 - - + +
307C TYR* 1.3 80.5 - - + +
309C LEU* 1.3 58.4 + - - +
311C SER* 3.2 17.5 + - - -
312C THR* 3.5 12.3 - - - +
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Residues in contact with LEU 309 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276C PRO* 3.7 28.3 - - + +
279C LEU* 3.9 25.1 - - + -
280C ALA* 3.6 37.9 - - + +
283C TYR* 4.2 7.2 - - + -
305C LYS 3.4 14.3 + - - +
306C PHE* 3.3 5.7 + - - +
307C TYR 3.1 0.6 - - - -
308C LYS* 1.3 79.9 - - - +
310C TYR* 1.3 59.2 + - - +
311C SER 3.3 0.7 - - - -
312C THR* 3.0 31.9 + - + +
313C ASN* 4.4 1.2 + - - +
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Residues in contact with TYR 310 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280C ALA* 5.9 4.0 - - + -
306C PHE* 2.9 41.4 + + + +
307C TYR* 3.2 5.4 + + - +
309C LEU* 1.3 74.6 - - - +
311C SER* 1.3 58.1 + - - +
312C THR 3.0 9.0 + - - -
313C ASN* 3.3 31.8 + - + +
315C ARG 3.7 5.0 + - - -
316C ALA* 3.5 28.8 - - + +
320C GLU* 2.4 43.3 + - + -
321C PHE* 3.7 16.1 - + - -
324C TYR* 3.7 30.1 - + - -
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Residues in contact with SER 311 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307C TYR* 3.0 21.0 + - - -
308C LYS* 3.2 19.4 + - - +
310C TYR* 1.3 76.9 - - - +
312C THR* 1.3 60.5 + - - +
313C ASN 3.5 2.6 - - - +
321C PHE* 3.5 28.0 - - - -
375C SER* 5.8 5.3 - - - -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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