Contacts of the helix formed by residues 303 - 314 (chain D) in PDB entry 4M3P
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 GLU 303 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35C LYS* 5.7 2.9 - - + +
36C ARG* 5.5 0.7 - - - +
32D ALA* 3.4 30.8 - - - +
35D LYS* 3.7 19.1 - - - +
36D ARG* 3.1 29.1 + - - -
63D PHE* 3.7 7.6 - - - -
301D GLY 3.9 10.3 - - - +
302D PHE* 1.3 74.9 - - - +
304D PRO* 1.3 77.7 - - + +
305D TYR* 3.3 18.2 - - + -
306D HIS* 2.9 32.6 + - + +
307D ILE* 3.3 3.8 + - - +
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Residues in contact with PRO 304 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35C LYS 3.6 12.6 - - - +
36C ARG* 4.0 15.9 - - + +
36D ARG* 4.0 5.6 - - - +
59D LEU* 4.4 2.0 - - + -
62D GLU* 3.5 45.5 - - + +
63D PHE* 3.9 22.7 - - + -
66D ALA* 3.2 11.2 - - + +
303D GLU* 1.3 98.6 - - + +
305D TYR* 1.3 58.4 + - - +
307D ILE 3.0 3.1 + - - -
308D ARG* 2.9 23.7 + - - -
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Residues in contact with TYR 305 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35C LYS* 3.0 57.7 + - + +
37C GLY* 6.5 0.4 - - - -
272C GLU* 2.8 37.4 + - - +
275D VAL* 4.2 2.8 - - - +
278D ARG* 3.5 40.9 - - + +
303D GLU* 3.9 15.3 - - + -
304D PRO* 1.3 74.0 - - - +
306D HIS* 1.3 98.2 + + - +
308D ARG* 3.5 33.3 + - - +
309D ALA* 3.0 25.3 + - - +
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Residues in contact with HIS 306 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250D ALA* 4.2 3.1 - - + -
275D VAL* 3.8 12.3 - - + +
276D ALA* 2.7 30.6 + - + +
277D THR 4.2 3.4 - - - -
278D ARG 4.6 0.4 - - - -
281D ILE* 3.3 35.2 - - + +
301D GLY 3.5 18.0 + - - -
302D PHE* 3.5 24.1 - + + -
303D GLU* 2.9 31.4 + - + +
305D TYR* 1.3 108.5 + + - +
307D ILE* 1.3 64.1 + - - +
309D ALA* 3.2 21.0 + - - +
310D ILE* 3.3 2.9 + - - +
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Residues in contact with ILE 307 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24D ILE* 3.7 15.2 - - + +
25D GLY 3.5 17.0 - - - +
26D ASP 3.8 15.3 - - - +
27D GLY* 4.1 1.3 - - - +
63D PHE* 3.6 30.1 - - + -
66D ALA* 3.7 20.7 - - + +
68D SER* 3.4 20.6 - - - +
298D GLY 4.7 1.8 - - - +
302D PHE* 3.9 18.8 - - + -
303D GLU 3.3 1.7 + - - +
304D PRO 3.0 8.1 + - - +
306D HIS* 1.3 75.1 - - - +
308D ARG* 1.3 65.1 + - - +
310D ILE* 3.2 26.4 + - + +
311D ALA* 3.2 10.0 + - - +
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Residues in contact with ARG 308 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34C GLU* 3.4 26.6 + - - -
37C GLY* 4.0 19.4 - - - -
66D ALA* 3.3 21.9 + - + +
278D ARG* 3.5 14.1 - - - +
304D PRO 2.9 12.4 + - - +
305D TYR* 3.7 26.6 + - - +
306D HIS 3.3 0.2 - - - -
307D ILE* 1.3 75.8 - - - +
309D ALA* 1.3 52.8 + - - +
311D ALA* 3.2 1.6 + - - +
312D GLU* 2.7 64.9 + - + +
322D PRO* 4.3 5.4 - - + -
324D ALA* 3.1 33.0 + - + +
325D SER* 4.2 6.5 - - - +
327D LYS* 3.6 16.4 + - - +
328D HIS* 3.5 19.7 - - - +
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Residues in contact with ALA 309 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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278D ARG* 3.4 35.0 - - + +
281D ILE* 3.9 9.9 - - + -
282D GLN* 3.4 13.4 - - + +
305D TYR 3.0 14.6 + - - +
306D HIS 3.2 11.4 - - - +
307D ILE 3.2 0.2 - - - -
308D ARG* 1.3 77.6 - - - +
310D ILE* 1.3 56.1 + - - +
312D GLU* 4.5 5.8 - - - +
313D GLU* 2.9 31.7 + - - +
328D HIS* 6.3 0.7 - - - -
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Residues in contact with ILE 310 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24D ILE* 4.2 13.5 - - + -
281D ILE* 3.7 12.6 - - + -
284D TYR* 4.4 2.7 - - + -
285D ALA* 3.8 17.5 - - + -
296D ILE* 3.7 46.0 - - + +
297D GLY 3.9 17.3 - - - +
302D PHE* 4.2 5.6 - - + -
306D HIS 3.6 9.6 - - - +
307D ILE* 3.2 30.2 + - + +
309D ALA* 1.3 75.7 - - - +
311D ALA* 1.3 63.9 + - - +
313D GLU* 3.3 1.0 + - - +
314D LEU* 3.1 33.1 + - + +
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Residues in contact with ALA 311 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24D ILE* 3.5 26.9 - - + -
66D ALA 3.7 20.4 - - - +
67D GLY* 4.5 1.8 - - - -
307D ILE 3.2 4.0 + - - +
308D ARG 3.7 6.1 - - - +
310D ILE* 1.3 80.7 - - - +
312D GLU* 1.3 56.8 + - - +
314D LEU* 3.7 2.5 - - - -
315D ALA* 3.0 27.0 + - - +
318D ARG* 4.7 6.5 + - - +
320D PHE 4.5 1.7 - - - +
322D PRO* 3.8 20.9 - - + +
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Residues in contact with GLU 312 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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394A LEU* 3.5 19.2 - - + +
398A PHE* 3.6 14.7 - - + -
282D GLN* 3.9 16.8 - - - +
308D ARG* 2.7 33.7 + - + +
309D ALA* 3.9 4.8 - - - +
311D ALA* 1.3 70.3 - - - +
313D GLU* 1.3 68.2 + - - +
314D LEU 3.2 0.4 - - - -
315D ALA* 3.2 19.9 + - - +
316D PRO* 4.1 0.9 - - - +
321D LEU* 4.1 9.0 - - + -
322D PRO* 4.6 0.7 - - + -
325D SER* 2.9 28.8 + - - +
328D HIS* 2.8 41.2 + - - -
329D GLY 4.3 2.6 - - - +
330D SER* 5.5 0.9 - - - -
331D TRP 5.6 0.5 + - - -
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Residues in contact with GLU 313 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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390A THR* 4.2 11.0 - - - +
394A LEU* 5.9 0.2 - - - -
282D GLN* 3.0 57.5 + - - +
285D ALA* 4.1 3.8 - - + -
286D ARG* 2.8 69.7 + - + +
309D ALA 2.9 19.3 + - - +
310D ILE 3.7 4.0 - - - +
312D GLU* 1.3 77.4 - - - +
314D LEU* 1.3 59.9 + - + +
315D ALA 3.3 0.6 + - - -
316D PRO* 3.7 6.8 - - - +
331D TRP* 4.1 9.5 + - - -
349D LYS* 5.7 3.3 + - - -
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Residues in contact with LEU 314 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22D ILE* 3.9 18.2 - - + -
24D ILE* 5.7 0.9 - - + -
285D ALA* 3.9 13.0 - - + +
286D ARG* 3.8 20.9 - - - +
289D TYR* 3.8 28.0 - - + -
296D ILE* 3.5 30.3 - - + -
310D ILE* 3.1 27.6 + - + +
311D ALA* 3.7 3.8 - - - +
313D GLU* 1.3 78.6 - - + +
315D ALA* 1.3 64.1 + - - +
316D PRO* 3.3 2.7 - - - -
317D GLU* 3.2 13.4 + - + +
318D ARG* 3.1 32.6 + - + +
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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