Contacts of the helix formed by residues 300 - 312 (chain P) in PDB entry 5D4C
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 300 (chain P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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292P ALA* 3.3 10.8 - - - +
298P GLY 3.6 5.9 + - - +
299P TRP* 1.3 73.6 - - - +
301P ALA* 1.3 63.2 + - - +
302P LYS* 3.2 31.6 + - - +
303P ARG* 3.2 21.6 + - - +
304P VAL* 3.3 24.9 + - - +
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Residues in contact with ALA 301 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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288P TYR* 3.6 34.3 - - + +
289P GLU* 3.7 29.8 - - + +
292P ALA* 3.7 3.4 - - - +
300P ASP* 1.3 73.0 - - - +
302P LYS* 1.3 60.0 + - - +
304P VAL* 3.1 6.9 + - - +
305P GLU* 2.9 27.8 + - - +
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Residues in contact with LYS 302 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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300P ASP* 3.2 16.1 + - - +
301P ALA* 1.3 78.9 - - - +
303P ARG* 1.3 59.6 + - - +
305P GLU* 3.3 15.9 + - - +
306P GLU* 2.9 29.3 + - + +
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Residues in contact with ARG 303 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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267P THR* 6.2 2.6 - - - +
297P PRO 4.8 0.6 + - - -
298P GLY* 3.4 28.1 + - - -
299P TRP* 3.4 58.2 - - + +
300P ASP* 3.2 21.9 + - - +
301P ALA 3.2 0.8 - - - -
302P LYS* 1.3 77.7 - - - +
304P VAL* 1.3 59.7 - - - +
306P GLU* 3.3 7.1 + - + +
307P THR* 2.9 37.0 + - - +
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Residues in contact with VAL 304 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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271P LEU* 4.1 7.0 - - + -
288P TYR* 3.8 29.4 - - + +
291P ILE* 3.7 40.6 - - + -
292P ALA 4.1 3.6 - - - +
299P TRP* 4.0 20.2 - - + -
300P ASP 3.3 16.2 - - - +
301P ALA 3.1 8.2 + - - +
303P ARG* 1.3 73.6 - - - +
305P GLU* 1.3 65.6 + - - +
307P THR* 3.3 3.8 + - - -
308P LEU* 2.9 40.8 + - + +
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Residues in contact with GLU 305 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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808M ARG* 2.6 49.8 + - - +
816M LYS 5.0 0.5 - - - +
817M PRO* 3.8 9.5 - - + +
818M GLY 3.7 13.3 + - - +
819M VAL 4.7 1.2 - - - +
288P TYR* 3.4 48.3 - - + +
301P ALA* 2.9 11.6 + - - +
302P LYS* 3.4 19.2 - - - +
304P VAL* 1.3 77.0 - - - +
306P GLU* 1.3 56.1 + - - +
308P LEU* 3.3 3.5 + - - +
309P LYS* 2.9 31.4 + - - +
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Residues in contact with GLU 306 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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716M LYS* 5.7 4.4 + - - -
302P LYS* 2.9 19.9 + - + +
303P ARG* 3.6 7.6 - - + +
305P GLU* 1.3 72.8 - - - +
307P THR* 1.3 60.9 + - - +
309P LYS* 3.3 19.0 + - - +
310P ILE* 2.9 38.2 + - + +
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Residues in contact with THR 307 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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264P MET* 6.2 1.6 - - - -
267P THR* 5.0 4.4 + - - +
268P ILE* 3.7 32.5 - - + +
271P LEU* 3.6 26.0 - - + -
299P TRP* 4.0 14.9 - - + -
303P ARG* 2.9 23.7 + - - +
304P VAL* 3.3 4.2 + - - -
306P GLU* 1.3 76.2 - - - +
308P LEU* 1.3 58.4 + - + +
310P ILE* 3.2 11.0 - - + +
311P ALA* 2.9 31.2 + - - +
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Residues in contact with LEU 308 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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817M PRO* 4.0 15.3 - - + -
268P ILE* 6.3 1.6 - - + -
271P LEU* 3.6 21.3 - - + -
272P SER* 5.9 3.6 - - - +
288P TYR* 3.7 29.8 - - + -
291P ILE* 5.1 6.7 - - + -
304P VAL* 2.9 27.4 + - + +
305P GLU 3.7 3.4 - - - +
307P THR* 1.3 76.1 - - + +
309P LYS* 1.3 63.0 + - - +
311P ALA* 3.4 6.9 + - + +
312P GLN* 3.2 28.8 + - - +
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Residues in contact with LYS 309 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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713M ARG* 5.3 6.6 - - - +
714M ASP 6.1 0.9 - - - -
817M PRO* 3.6 32.8 + - + +
818M GLY* 4.3 11.2 - - - +
532N GLY 4.9 4.9 + - - -
533N GLY* 4.5 20.0 + - - -
534N ARG* 4.9 4.2 - - - +
305P GLU 2.9 17.2 + - - +
306P GLU* 3.3 20.2 + - - +
308P LEU* 1.3 78.4 - - - +
310P ILE* 1.3 64.2 + - + +
311P ALA 3.5 0.5 + - - -
312P GLN* 3.6 33.3 + - - +
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Residues in contact with ILE 310 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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716M LYS* 5.9 3.1 - - - +
34N TYR* 3.3 54.2 - - + +
35N ARG* 4.7 14.8 - - + +
256P ARG* 4.8 0.7 + - - -
260P ILE* 4.8 12.0 - - + +
264P MET* 5.1 11.9 - - + -
268P ILE* 4.7 10.7 - - + +
306P GLU* 2.9 25.7 + - + +
307P THR* 3.2 20.4 - - + +
309P LYS* 1.3 79.8 - - + +
311P ALA* 1.3 61.3 + - - +
312P GLN 3.3 3.7 + - - +
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Residues in contact with ALA 311 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256P ARG* 2.5 35.1 + - - +
268P ILE* 3.7 36.8 - - + -
307P THR 2.9 18.1 + - - +
308P LEU* 3.8 10.3 - - + +
309P LYS 3.3 0.4 - - - -
310P ILE* 1.3 78.8 - - - +
312P GLN* 1.3 60.5 + - - +
313P GLU* 3.3 2.3 + - - +
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Residues in contact with GLN 312 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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816M LYS* 5.8 0.8 - - - +
817M PRO* 4.2 28.9 + - - +
534N ARG* 3.1 37.9 + - + +
256P ARG* 4.8 0.5 + - - -
258P ILE* 6.1 0.5 - - - +
308P LEU* 3.2 17.7 + - - +
309P LYS* 3.7 32.2 + - - +
310P ILE 3.3 5.2 - - - +
311P ALA* 1.3 77.6 - - - +
313P GLU* 1.3 61.3 + - - +
314P PRO* 4.0 2.9 - - - +
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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