Contacts of the helix formed by residues 317 - 322 (chain D) in PDB entry 2JG3
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 317 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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230A ILE* 3.6 29.4 - - + +
231A LEU* 4.1 20.5 + - + +
315D PRO* 3.4 25.4 - - + +
316D LYS* 1.3 79.3 - - - +
318D ARG* 1.3 75.5 + - - +
319D ALA 3.5 0.2 - - - -
320D LYS* 3.6 27.6 - - - +
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Residues in contact with ARG 318 (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 HIS* 3.7 6.7 + - - -
279D PRO* 4.0 17.4 - - - +
280D ALA* 3.5 31.1 - - + +
314D MET* 3.6 17.9 - - + +
315D PRO* 3.1 16.7 + - + +
317D GLU* 1.3 99.1 - - - +
319D ALA* 1.3 64.6 + - - +
320D LYS 3.2 2.5 - - - -
321D GLU* 2.9 63.0 + - - +
322D LEU* 4.2 1.0 + - - +
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Residues in contact with ALA 319 (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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314D MET* 3.9 12.1 - - - -
315D PRO 3.5 3.2 + - - +
316D LYS 3.2 16.0 + - - +
318D ARG* 1.3 77.9 - - - +
320D LYS* 1.3 57.0 + - - +
321D GLU 3.0 0.2 - - - -
322D LEU* 3.0 20.5 + - - +
326D TYR* 3.2 34.6 - - + +
349D ALA 5.3 0.7 - - - +
350D TYR 4.6 1.1 - - - -
351D PRO* 3.7 36.6 - - + -
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Residues in contact with LYS 320 (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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316D LYS 4.7 1.0 + - - -
317D GLU 3.6 22.7 - - - +
318D ARG 4.6 0.9 - - - -
319D ALA* 1.3 76.9 - - - +
321D GLU* 1.3 69.2 + - + +
322D LEU 3.3 0.2 - - - -
323D ARG 3.2 27.5 + - - +
324D ASP* 3.5 11.3 + - + +
326D TYR* 4.2 2.8 - - - +
327D ALA* 3.8 31.8 - - + +
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Residues in contact with GLU 321 (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 HIS* 2.9 30.6 - - + -
318D ARG* 2.9 61.6 + - - +
320D LYS* 1.3 88.5 - - + +
322D LEU* 1.3 59.6 + - - +
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Residues in contact with LEU 322 (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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270D ALA* 4.2 8.1 - - + -
274D GLU* 3.6 43.1 - - + +
275D PHE* 3.6 34.1 - - + +
278D HIS* 4.3 18.6 - - + +
314D MET* 3.6 28.9 - - + -
318D ARG 4.5 0.7 - - - +
319D ALA 3.0 10.4 + - - +
321D GLU* 1.3 79.4 - - - +
323D ARG* 1.3 83.7 + - - +
326D TYR* 4.0 11.7 - - + -
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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