Contacts of the helix formed by residues 322 - 328 (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 PRO 322 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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65D ARG 3.6 1.1 - - - +
66D ALA 3.4 35.7 - - - +
67D GLY* 3.6 9.0 - - - -
308D ARG* 4.3 8.7 - - + +
311D ALA* 3.8 23.8 - - + +
312D GLU* 4.6 0.2 - - + -
318D ARG* 5.8 1.3 - - - +
320D PHE* 4.6 5.8 - - + +
321D LEU* 1.3 92.9 - - + +
323D PRO* 1.4 73.2 - - + +
325D SER* 3.0 39.9 + - - +
326D GLU 4.4 0.5 + - - -
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Residues in contact with PRO 323 (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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64D LEU 4.5 4.7 - - - +
65D ARG* 3.2 42.4 - - + +
67D GLY* 4.9 1.6 - - - +
321D LEU 3.9 1.3 - - - +
322D PRO* 1.4 82.3 - - + +
324D ALA* 1.3 53.8 + - - +
325D SER 3.1 0.5 + - - -
326D GLU* 2.6 39.9 + - + +
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Residues in contact with ALA 324 (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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37C GLY* 4.4 8.7 - - - -
65D ARG* 2.9 45.1 + - + +
66D ALA* 3.9 11.4 - - + +
308D ARG* 3.1 39.9 + - + +
322D PRO* 3.2 1.0 + - + -
323D PRO* 1.3 75.1 - - - +
325D SER* 1.3 57.2 + - - +
326D GLU 3.1 0.2 - - - -
327D LYS* 3.0 19.9 + - - +
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Residues in contact with SER 325 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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398A PHE* 3.4 19.8 - - - -
308D ARG* 4.2 0.3 - - - +
312D GLU* 2.9 29.8 + - - +
321D LEU* 3.8 16.6 - - - +
322D PRO* 3.0 34.9 + - - +
324D ALA* 1.3 71.9 - - - +
326D GLU* 1.3 60.1 + - - +
327D LYS 3.0 2.2 - - - -
328D HIS* 3.0 25.2 + - - +
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Residues in contact with GLU 326 (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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401A GLN 6.1 5.6 - - - -
40C LYS* 4.5 7.8 + - - +
51C GLU* 4.7 4.0 - - - +
52C HIS* 4.7 3.8 + - - -
65D ARG* 3.0 27.6 + - - +
322D PRO 4.4 0.6 + - - -
323D PRO* 2.6 29.1 + - + +
325D SER* 1.3 77.4 - - - +
327D LYS* 1.3 80.0 + - + +
328D HIS 3.3 3.1 + - - +
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Residues in contact with LYS 327 (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* 4.6 1.2 - - - +
37C GLY 3.5 23.6 - - - +
38C TYR* 3.7 19.1 - - - +
39C VAL 3.4 16.9 - - - +
40C LYS* 3.3 33.1 - - + +
41C ALA 4.3 1.6 + - - -
47C GLU* 2.8 31.2 + - - +
51C GLU* 2.8 31.7 + - - -
52C HIS* 5.7 1.3 - - - -
65D ARG* 3.6 10.3 - - - +
308D ARG* 3.6 5.9 + - - +
324D ALA 3.0 11.2 + - - +
326D GLU* 1.3 97.0 + - - +
328D HIS* 1.3 60.4 + - - +
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Residues in contact with HIS 328 (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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398A PHE* 3.8 4.0 - - - -
34C GLU* 4.0 5.6 - - - -
40C LYS* 3.5 24.9 + - - +
41C ALA* 5.9 1.8 - - + -
269C PHE* 4.2 15.0 - + - -
278D ARG* 3.0 46.8 + - + -
279D TRP* 4.6 10.7 - + - -
282D GLN* 5.2 0.4 - - - -
308D ARG* 3.5 26.0 - - - +
309D ALA* 6.3 0.2 - - - -
312D GLU* 2.8 40.9 + - - +
325D SER* 3.0 16.5 + - - +
326D GLU 4.5 1.2 - - - +
327D LYS* 1.3 79.2 - - - +
329D GLY* 1.3 73.8 + - - +
331D TRP 5.5 0.2 - - - -
332D GLY 5.6 0.6 + - - -
334D GLY* 5.8 0.2 - - - -
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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