Contacts of the helix formed by residues 300 - 315 (chain B) in PDB entry 5M64
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 300 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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297B VAL 5.3 0.9 + - - -
298B LYS 3.4 4.7 + - - -
299B ASP* 1.3 72.3 - - - +
301B PHE* 1.3 56.1 + - - +
302B LEU 3.0 6.3 - - - -
303B THR* 2.9 21.5 + - - -
304B ASP* 2.9 23.1 + - - +
47I VAL* 3.2 25.6 - - - +
48I VAL* 2.4 31.6 + - - +
49I THR* 3.5 20.3 - - - +
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Residues in contact with PHE 301 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1486A VAL* 5.5 12.8 - - + -
252B TYR* 4.9 0.9 - - - -
299B ASP* 3.5 10.3 - - + +
300B SER* 1.3 76.8 - - - +
302B LEU* 1.3 55.6 + - - +
304B ASP* 2.8 25.9 - - - +
305B ARG* 3.2 35.5 - - + +
379B ARG* 6.2 0.9 - - - -
382B TYR* 4.3 10.7 - + + -
385B VAL* 3.9 36.1 - - + -
386B ALA* 4.0 25.6 - - + -
49I THR* 5.2 1.4 - - - +
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Residues in contact with LEU 302 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289B PHE* 3.7 31.4 - - + -
292B ILE* 3.6 24.9 - - + -
293B ILE* 3.2 39.3 - - + +
296B ASP 5.3 4.3 - - - +
297B VAL* 6.3 3.4 - - + -
299B ASP* 4.1 24.6 + - - +
300B SER 3.0 0.8 - - - -
301B PHE* 1.3 78.8 - - - +
303B THR* 1.3 61.5 + - - +
305B ARG* 3.5 1.8 + - - +
306B LEU* 2.9 44.3 + - + +
379B ARG* 4.4 13.1 + - - +
382B TYR* 6.3 0.4 - - - -
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Residues in contact with THR 303 (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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1482A LYS* 4.8 6.7 - - - +
289B PHE* 5.9 3.0 - - - -
297B VAL* 4.8 13.7 + - - +
299B ASP 4.4 3.5 + - - -
300B SER* 2.9 23.1 + - - -
302B LEU* 1.3 82.6 - - - +
304B ASP* 1.3 58.8 + - - +
306B LEU* 4.8 2.5 - - - -
307B GLU* 2.9 66.4 + - + +
4I VAL 5.4 0.7 - - - +
5I GLY* 4.7 9.4 - - - -
6I SER* 4.4 11.7 - - - +
47I VAL* 5.0 7.1 - - + +
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Residues in contact with ASP 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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1482A LYS* 3.7 30.0 - - + +
1483A LEU 4.7 1.3 - - - +
1484A LEU* 3.3 28.2 - - + +
1485A MET 5.7 0.3 + - - -
1486A VAL* 5.6 5.7 - - - +
300B SER* 2.9 14.6 + - - +
301B PHE* 2.8 30.6 - - - +
303B THR* 1.3 74.1 - - - +
305B ARG* 1.3 78.3 + - - +
307B GLU* 4.4 0.2 - - - +
308B LEU* 3.1 32.2 + - - +
49I THR* 5.5 8.8 - - + +
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Residues in contact with ARG 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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1484A LEU* 4.6 11.0 - - - -
252B TYR* 2.3 51.6 + - - -
253B LEU 3.9 0.4 + - - -
256B GLY* 2.9 48.1 + - - +
257B GLN 3.8 6.3 + - - -
258B VAL* 5.6 1.4 - - - +
301B PHE* 3.2 42.6 - - + +
302B LEU* 3.5 1.7 + - - +
303B THR 3.3 0.6 - - - -
304B ASP* 1.3 95.2 + - - +
306B LEU* 1.3 58.8 + - - +
308B LEU* 3.6 2.6 + - - +
309B LEU* 2.9 30.0 + - - +
381B LEU* 6.0 0.2 - - - +
382B TYR* 3.6 35.3 + - + -
385B VAL* 4.5 0.8 - - - +
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Residues in contact with LEU 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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288B ILE* 5.4 5.2 - - + -
289B PHE* 3.6 44.4 - - + +
292B ILE* 3.7 27.1 - - + -
302B LEU* 2.9 25.6 + - + +
303B THR* 4.2 1.8 - - - +
305B ARG* 1.3 76.0 - - - +
307B GLU* 1.3 75.3 + - + +
309B LEU* 3.2 7.8 + - + +
310B LEU* 3.0 26.7 + - + +
379B ARG* 5.1 4.3 - - - +
382B TYR* 5.3 3.1 - - - -
7I LEU* 6.4 1.3 - - + -
9I PHE* 5.3 7.6 - - + -
16I LEU* 5.5 8.7 - - + -
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Residues in contact with GLU 307 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1482A LYS* 3.7 31.5 + - + +
303B THR* 2.9 39.1 + - + +
304B ASP 4.4 1.8 - - - +
306B LEU* 1.3 84.4 - - + +
308B LEU* 1.3 57.1 + - - +
310B LEU* 4.3 2.9 - - - +
311B ARG* 2.8 33.4 + - - +
4I VAL 4.8 0.3 - - - +
6I SER* 3.4 19.1 + - - +
7I LEU* 3.3 37.4 + - + +
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Residues in contact with LEU 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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1482A LYS* 4.7 26.1 - - + +
1484A LEU* 3.8 24.2 - - + -
255B ASP* 3.4 30.5 - - - +
256B GLY* 3.7 10.3 - - - -
257B GLN* 3.3 28.3 + - - +
304B ASP 3.1 20.0 + - - +
305B ARG* 4.0 5.2 - - - +
306B LEU 3.3 0.2 - - - -
307B GLU* 1.3 78.7 - - - +
309B LEU* 1.3 57.0 + - - +
311B ARG* 4.0 5.2 - - + +
312B GLY* 2.9 23.9 + - - -
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Residues in contact with LEU 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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256B GLY 4.8 2.5 - - - +
257B GLN* 4.1 29.6 - - + -
258B VAL* 4.3 7.0 - - + +
272B PRO* 6.5 0.7 - - + -
273B VAL* 4.0 24.7 - - + -
274B VAL* 3.7 23.5 - - + +
305B ARG 2.9 18.9 + - - +
306B LEU* 3.6 8.3 - - + +
307B GLU 3.2 0.2 - - - -
308B LEU* 1.3 75.1 - - - +
310B LEU* 1.3 71.7 + - + +
312B GLY* 3.1 11.4 + - - -
313B PHE* 3.2 11.1 + - - +
378B ILE* 5.8 2.2 - - + -
382B TYR* 4.4 13.0 - - - +
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Residues in contact with LEU 310 (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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274B VAL* 4.9 8.1 - - + -
278B LYS* 6.4 0.4 - - + -
288B ILE* 6.0 6.1 - - + -
306B LEU* 3.0 18.3 + - + +
307B GLU* 4.3 2.7 - - - +
309B LEU* 1.3 80.7 - - + +
311B ARG* 1.3 61.2 + - - +
313B PHE* 2.9 38.5 + - + +
314B LYS* 2.9 23.6 + - + +
16I LEU* 3.6 47.6 - - + -
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Residues in contact with ARG 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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1481A GLU* 4.3 30.3 - - + +
1482A LYS* 6.1 2.7 - - + -
307B GLU 2.8 21.0 + - - +
308B LEU* 4.0 6.7 - - + +
310B LEU* 1.3 78.1 - - - +
312B GLY* 1.3 56.8 + - - +
314B LYS* 3.9 20.4 - - - +
315B LYS* 3.0 35.8 + - + +
7I LEU* 4.9 8.7 - - - +
16I LEU* 5.6 3.6 - - - +
17I LEU 4.1 5.0 + - - -
18I GLU* 3.4 24.1 + - - +
19I ASN* 3.1 48.3 + - - +
22I ALA* 5.7 2.8 - - - +
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Residues in contact with GLY 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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257B GLN* 4.2 17.1 - - - +
308B LEU 2.9 17.1 + - - -
309B LEU 3.1 6.8 + - - -
311B ARG* 1.3 75.6 - - - +
313B PHE* 1.3 57.3 + - - +
315B LYS* 3.4 33.2 - - - +
316B ARG* 4.2 5.4 - - - +
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Residues in contact with PHE 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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274B VAL* 3.5 49.4 - - + -
275B MET* 4.9 6.7 - - - -
278B LYS* 4.1 20.2 - - + -
309B LEU 3.2 4.0 + - - +
310B LEU* 2.9 26.0 + - + +
312B GLY* 1.3 79.1 - - - +
314B LYS* 1.3 66.9 + - + +
315B LYS 3.4 0.6 + - - -
316B ARG* 3.7 33.6 + - - +
317B TYR 3.8 12.1 + - - +
320B LEU* 3.4 40.2 - - + -
321B GLN* 5.6 0.7 - - - -
326B VAL* 5.1 1.3 - - + -
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Residues in contact with LYS 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 LEU* 2.9 23.1 + - + +
311B ARG* 4.1 24.4 - - - +
313B PHE* 1.3 78.8 - - + +
315B LYS* 1.3 67.0 + - - +
316B ARG 3.2 1.2 + - - -
317B TYR 5.0 3.4 - - - -
318B PRO* 3.5 39.3 - - + +
18I GLU* 3.8 30.5 - - + +
23I VAL* 5.2 7.5 - - - +
31I SER* 5.3 11.4 - - - +
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Residues in contact with LYS 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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257B GLN* 5.3 5.2 - - - +
311B ARG* 3.0 26.7 + - + +
312B GLY* 3.4 26.5 - - - +
314B LYS* 1.3 79.8 - - - +
316B ARG* 1.3 74.6 + - - +
318B PRO* 4.8 4.0 - - - +
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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