Contacts of the helix formed by residues 299 - 312 (chain A) in PDB entry 4HRE
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 299 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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24A TYR* 3.5 9.2 - - + -
266A LYS* 4.4 3.1 - - - +
267A PRO* 4.1 16.5 - - + +
270A PHE* 4.0 11.1 - - - -
295A ARG* 2.7 45.8 + - - +
298A VAL* 1.3 79.4 - - + +
300A MET* 1.3 54.0 + - - +
301A LEU 3.2 2.5 - - - -
302A LYS* 2.7 46.0 + - - +
303A ILE* 3.3 24.5 + - - +
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Residues in contact with MET 300 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A TYR 3.4 2.6 + - - -
26A SER* 3.5 26.2 - - - +
274A LEU* 5.5 0.2 - - + -
291A ILE* 3.8 19.7 - - + +
292A MET* 3.8 42.6 - - + +
295A ARG* 3.1 27.2 + - + +
296A SER* 3.6 14.1 - - - +
298A VAL 3.6 0.4 - - - -
299A ASP* 1.3 75.3 + - - +
301A LEU* 1.3 61.2 + - - +
302A LYS 3.2 0.2 + - - -
303A ILE* 3.3 16.1 + - + -
304A ARG* 2.9 24.2 + - - +
315A LEU* 4.2 15.3 - - - -
334A LEU 3.9 1.3 - - - +
335A CYS 3.6 10.1 - - - +
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Residues in contact with LEU 301 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A ALA 3.6 22.9 - - - +
24A TYR* 2.8 34.0 + - + +
25A GLY 3.5 14.4 - - - +
26A SER* 3.9 9.0 - - - -
28A LYS* 5.2 1.8 - - - +
300A MET* 1.3 70.8 - - - +
302A LYS* 1.3 59.1 + - + +
304A ARG* 3.2 35.9 + - - +
305A SER* 2.8 29.0 + - - +
339A ASP* 5.1 1.0 - - - +
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Residues in contact with LYS 302 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A TYR* 3.3 59.0 + - + -
267A PRO* 3.8 28.6 - - + +
299A ASP* 2.7 20.9 + - - +
301A LEU* 1.3 70.3 - - + +
303A ILE* 1.3 54.5 + - - +
304A ARG 3.1 1.1 - - - -
305A SER* 2.9 11.7 + - - +
306A GLU* 2.8 39.4 + - + +
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Residues in contact with ILE 303 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267A PRO* 3.8 18.8 - - + +
270A PHE* 3.7 15.5 - - + -
271A ALA* 3.5 21.4 - - - +
274A LEU* 3.5 27.8 - - + -
291A ILE* 4.7 2.2 - - + -
295A ARG* 3.6 20.4 - - + -
299A ASP* 3.3 35.3 + - - +
300A MET* 3.5 20.6 - - + +
302A LYS* 1.3 76.0 - - - +
304A ARG* 1.3 58.5 + - - +
306A GLU* 3.4 0.9 + - - -
307A PHE* 2.7 31.9 + - + +
315A LEU* 5.2 1.6 - - + -
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Residues in contact with ARG 304 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300A MET* 2.9 19.9 + - - +
301A LEU* 3.3 34.9 - - - +
302A LYS 3.1 0.2 - - - -
303A ILE* 1.3 78.6 - - - +
305A SER* 1.3 60.5 + - - +
307A PHE* 3.2 7.0 + - - +
308A LYS* 3.2 22.5 + - - +
315A LEU* 4.1 26.7 + - + -
335A CYS* 3.1 33.6 + - - -
336A GLY* 3.6 11.3 + - - -
337A GLY* 3.2 36.0 + - - -
338A ASP 3.7 5.5 + - - +
339A ASP* 2.7 46.7 + - - +
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Residues in contact with SER 305 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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301A LEU* 2.8 19.1 + - - +
302A LYS* 2.9 17.5 + - - +
304A ARG* 1.3 79.2 - - - +
306A GLU* 1.3 64.0 + - - +
308A LYS* 3.7 4.0 + - - +
309A ARG* 3.5 19.8 + - - +
339A ASP* 5.2 5.4 + - - -
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Residues in contact with GLU 306 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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265A ASN* 3.3 26.3 + - - +
267A PRO* 4.0 5.8 - - + +
268A LEU* 3.8 38.6 - - + +
271A ALA* 4.5 2.6 - - + +
302A LYS* 2.8 22.9 + - - +
303A ILE 3.9 3.1 - - - +
305A SER* 1.3 74.8 - - - +
307A PHE* 1.3 64.7 + - - +
309A ARG* 3.3 34.6 + - - +
310A LYS* 3.2 26.9 + - - +
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Residues in contact with PHE 307 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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271A ALA* 3.7 35.9 - - + +
274A LEU* 4.5 2.2 - - + -
275A TYR* 3.8 25.6 - + + -
278A MET* 5.0 0.7 - - + -
303A ILE* 2.7 24.1 + - + +
304A ARG* 3.2 8.9 + - - +
306A GLU* 1.3 75.4 - - - +
308A LYS* 1.3 59.0 + - - +
311A TYR* 3.3 32.0 + + + +
313A LYS 3.2 13.7 - - - +
314A SER 3.7 2.2 - - - -
315A LEU* 3.4 35.7 - - + +
318A TYR* 3.2 48.7 - + + -
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Residues in contact with LYS 308 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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304A ARG 3.2 13.8 + - - +
305A SER* 4.3 4.0 - - - +
306A GLU 3.2 0.2 - - - -
307A PHE* 1.3 77.4 - - - +
309A ARG* 1.3 60.2 + - - +
312A GLY* 2.9 40.3 + - - +
313A LYS* 3.5 19.8 + - - +
314A SER* 4.1 8.2 - - - +
339A ASP* 2.7 49.6 + - + +
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Residues in contact with ARG 309 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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265A ASN* 5.1 2.4 - - - +
268A LEU* 4.4 15.4 - - - +
305A SER 3.5 12.6 + - - +
306A GLU* 3.3 33.7 + - - +
308A LYS* 1.3 81.4 - - - +
310A LYS* 1.3 77.4 + - - +
312A GLY* 4.2 2.6 + - - -
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Residues in contact with LYS 310 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268A LEU* 4.1 20.2 - - + +
272A ASP* 3.4 33.0 + - - +
306A GLU 3.2 12.2 + - - +
309A ARG* 1.3 91.3 - - - +
311A TYR* 1.3 93.5 + - + +
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Residues in contact with TYR 311 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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271A ALA* 4.1 8.1 - - + -
272A ASP* 3.4 24.6 + - - +
275A TYR* 3.4 58.3 - + + +
276A ASP* 5.4 0.5 + - - -
307A PHE* 3.3 45.8 + + + +
310A LYS* 1.3 111.1 - - + +
312A GLY* 1.3 56.8 + - - +
313A LYS* 3.0 11.8 + - - +
318A TYR* 4.0 20.0 + - - +
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Residues in contact with GLY 312 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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308A LYS* 2.9 33.6 + - - +
309A ARG 4.2 2.0 + - - -
310A LYS 3.5 1.8 - - - -
311A TYR* 1.3 75.8 - - - +
313A LYS* 1.3 66.6 + - - +
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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