Contacts of the helix formed by residues 285 - 300 (chain C) in PDB entry 4H9Q
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 285 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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108A ASN* 3.3 18.8 - - - +
116A ARG* 2.7 35.1 + - - +
39B ARG* 5.9 0.2 - - - +
42B GLY 3.5 13.1 + - - +
44B LYS* 3.1 16.0 + - - +
283C PHE 3.9 0.2 + - - -
284C PRO* 1.3 75.7 - - - +
286C TYR* 1.3 65.2 + - - +
287C GLY 3.9 2.7 - - - -
288C ASP* 2.9 43.8 + - - +
289C VAL* 3.2 12.6 + - - +
317C PHE* 3.6 4.5 - - - -
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Residues in contact with TYR 286 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108A ASN* 4.1 0.8 + - - -
111A THR 3.7 19.4 + - - +
112A ILE* 3.9 16.8 - - + -
113A HIS 3.4 36.3 - - - -
114A ALA* 4.5 1.6 - - - -
285C ASP* 1.3 73.7 - - - +
287C GLY* 1.3 59.8 + - - +
289C VAL* 3.2 2.4 + - - -
290C LEU* 2.9 49.7 + - + +
310C GLN* 3.5 22.3 + - - +
313C ALA* 3.7 18.9 - - + +
314C GLN* 3.4 40.9 + - + -
317C PHE* 3.4 38.4 - + + -
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Residues in contact with GLY 287 (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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113A HIS 5.2 3.5 + - - -
114A ALA 5.8 2.7 - - - -
116A ARG* 3.5 21.4 + - - +
285C ASP* 3.1 8.8 + - - -
286C TYR* 1.3 84.1 - - - +
288C ASP* 1.3 55.9 + - - +
290C LEU* 3.8 8.2 - - - +
291C ARG* 2.9 31.2 + - - +
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Residues in contact with ASP 288 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116A ARG* 3.1 15.3 + - - +
39B ARG* 5.0 4.0 + - - -
44B LYS* 3.3 21.1 + - - +
274C LEU* 3.8 16.3 - - + +
283C PHE 4.9 0.2 - - - +
284C PRO* 3.4 20.0 - - + +
285C ASP* 2.9 42.3 + - - +
287C GLY* 1.3 74.5 - - - +
289C VAL* 1.3 58.9 + - - +
291C ARG* 3.3 9.5 + - - +
292C ALA* 2.9 27.9 + - - +
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Residues in contact with VAL 289 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271C ILE* 4.6 10.1 - - + -
274C LEU* 3.9 20.0 - - + -
284C PRO* 4.1 9.0 - - + -
285C ASP 3.2 11.0 + - - +
286C TYR 3.2 6.5 + - - +
288C ASP* 1.3 77.8 - - - +
290C LEU* 1.3 57.1 + - - +
292C ALA* 3.1 3.7 + - - +
293C VAL* 2.9 31.7 + - + +
313C ALA* 3.7 26.5 - - - +
316C ALA* 4.0 18.6 - - + -
317C PHE* 3.8 26.5 - - + +
320C VAL* 4.8 5.8 - - + -
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Residues in contact with LEU 290 (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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114A ALA* 4.5 25.1 - - + +
286C TYR* 2.9 43.7 + - + +
287C GLY* 3.8 7.4 - - - +
289C VAL* 1.3 76.6 - - - +
291C ARG* 1.3 56.9 + - - +
293C VAL* 3.4 1.8 + - + +
294C GLU* 2.9 62.6 + - + +
309C LEU* 4.2 12.3 - - + +
310C GLN* 4.3 14.6 - - + -
313C ALA* 3.7 25.9 - - + +
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Residues in contact with ARG 291 (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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116A ARG* 6.0 2.0 - - - +
287C GLY 2.9 17.7 + - - +
288C ASP* 3.6 10.1 - - - +
289C VAL 3.2 0.2 - - - -
290C LEU* 1.3 75.3 - - - +
292C ALA* 1.3 59.2 + - - +
294C GLU* 4.1 10.5 - - - +
295C LYS* 2.9 77.5 + - + +
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Residues in contact with ALA 292 (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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270C ARG* 3.9 30.9 - - + +
271C ILE* 4.6 8.7 - - + -
274C LEU* 4.3 17.7 - - + -
288C ASP 2.9 14.0 + - - +
289C VAL* 3.1 9.6 + - - +
291C ARG* 1.3 77.2 - - - +
293C VAL* 1.3 56.5 + - - +
295C LYS* 3.9 2.6 - - - +
296C ALA* 2.9 31.7 + - - +
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Residues in contact with VAL 293 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267C VAL* 3.9 25.9 - - + +
271C ILE* 4.0 15.0 - - + -
289C VAL* 2.9 19.8 + - + +
290C LEU* 3.8 6.3 - - + +
292C ALA* 1.3 75.9 - - - +
294C GLU* 1.3 56.3 + - - +
296C ALA* 3.7 2.0 - - - +
297C ALA* 2.9 28.8 + - - +
309C LEU* 3.6 34.5 - - + +
312C MET* 4.0 20.9 - - + -
313C ALA* 4.2 20.4 - - + +
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Residues in contact with GLU 294 (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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290C LEU* 2.9 51.1 + - + +
291C ARG* 3.8 12.7 - - - +
293C VAL* 1.3 74.9 - - - +
295C LYS* 1.3 63.9 + - + +
297C ALA* 3.3 2.1 + - - +
298C ALA* 2.9 32.2 + - - +
309C LEU* 4.0 26.6 - - + +
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Residues in contact with LYS 295 (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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270C ARG* 5.5 3.1 - - + -
291C ARG* 2.9 71.5 + - + +
292C ALA* 3.9 4.5 - - - +
294C GLU* 1.3 80.2 + - + +
296C ALA* 1.3 61.2 + - - +
298C ALA* 3.9 4.3 - - + +
299C ARG* 2.9 33.7 + - - +
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Residues in contact with ALA 296 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266C GLU* 4.1 8.3 - - + +
267C VAL* 3.8 33.7 - - + +
270C ARG* 4.1 11.3 - - + +
292C ALA 2.9 19.2 + - - +
293C VAL 3.7 3.6 - - - +
295C LYS* 1.3 75.4 - - - +
297C ALA* 1.3 63.5 + - - +
299C ARG* 3.8 4.4 - - - +
300C HIS* 3.1 32.7 + - - +
302C LEU* 4.5 2.3 - - - +
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Residues in contact with ALA 297 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267C VAL* 4.8 1.1 - - + +
293C VAL 2.9 18.3 + - - +
294C GLU* 3.7 4.3 - - - +
296C ALA* 1.3 76.8 - - - +
298C ALA* 1.3 57.7 + - - +
301C SER* 3.1 8.7 + - - -
302C LEU* 3.0 47.6 + - + +
303C GLY 4.6 0.9 + - - +
304C LEU* 4.5 10.1 - - + +
309C LEU* 3.8 26.2 - - + -
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Residues in contact with ALA 298 (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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294C GLU 2.9 18.3 + - - +
295C LYS* 3.9 5.6 - - + +
297C ALA* 1.3 74.2 - - - +
299C ARG* 1.3 66.6 + - - +
301C SER* 3.4 14.2 + - - +
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Residues in contact with ARG 299 (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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295C LYS 2.9 19.8 + - - +
296C ALA* 3.8 3.4 - - - +
298C ALA* 1.3 79.3 - - - +
300C HIS* 1.3 93.7 + - + +
301C SER* 3.5 4.0 + - - -
402C PO4 4.5 12.2 + - - +
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Residues in contact with HIS 300 (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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266C GLU* 3.6 32.5 - - + +
269C ARG* 4.7 2.2 + - - -
296C ALA* 3.1 21.0 + - - +
299C ARG* 1.3 115.9 + - + +
301C SER* 1.3 69.9 + - - +
302C LEU* 3.2 23.9 + - + +
402C PO4 3.1 40.6 + - - -
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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