Contacts of the helix formed by residues 318 - 329 (chain D) in PDB entry 4P0S
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 ALA 318 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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316D LEU 3.7 0.4 + - - -
317D ARG* 1.3 77.6 - - + +
319D GLU* 1.3 63.0 + - - +
320D ALA 3.4 0.3 + - - -
321D PHE* 3.4 10.4 + - - +
322D VAL* 3.4 17.9 + - - +
363D ILE* 3.9 12.5 - - + +
364D VAL 3.0 25.5 + - - +
365D ASP* 3.7 28.5 - - + +
368D LYS* 5.6 4.5 - - - +
369D CYS* 5.3 4.8 - - - -
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Residues in contact with GLU 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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317D ARG* 3.6 30.0 - - - +
318D ALA* 1.3 77.0 - - - +
320D ALA* 1.3 70.3 + - - +
322D VAL* 3.3 10.4 + - - +
323D SER* 3.0 25.3 + - - -
368D LYS* 5.7 4.0 - - - +
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Residues in contact with ALA 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 LEU* 4.2 17.9 - - + -
317D ARG* 3.1 13.9 + - + +
319D GLU* 1.3 89.8 - - - +
321D PHE* 1.3 64.1 + - - +
323D SER* 3.1 16.5 + - - -
324D MET* 3.2 24.2 + - + +
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Residues in contact with PHE 321 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316D LEU* 4.0 24.8 - - + +
317D ARG 3.4 4.9 + - - +
318D ALA 3.4 8.4 + - - +
319D GLU 3.2 0.4 - - - -
320D ALA* 1.3 73.4 - - - +
322D VAL* 1.3 69.9 + - + +
324D MET* 3.1 14.1 + - - +
325D ILE* 3.2 25.6 + - + +
343D LEU* 3.8 30.7 - - + -
361D LEU* 5.0 4.9 - - + -
363D ILE* 3.7 33.0 - - + -
369D CYS* 5.0 12.8 - - - -
408D ALA* 3.9 23.3 - - + -
411D ALA* 3.9 15.5 - - + -
412D LEU* 3.3 35.4 - - + -
415D LEU* 5.0 1.6 - - + -
425D ILE* 6.1 0.9 - - + -
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Residues in contact with VAL 322 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318D ALA 3.4 14.8 + - - +
319D GLU* 3.3 9.8 + - - +
321D PHE* 1.3 81.3 - - + +
323D SER* 1.3 63.1 + - - +
325D ILE* 3.3 12.1 + - + +
326D ASP* 3.2 25.3 + - + +
368D LYS* 4.2 23.8 - - - +
369D CYS* 4.4 16.4 - - - -
403D VAL* 4.1 36.1 - - + +
408D ALA* 6.5 0.4 - - + -
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Residues in contact with SER 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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319D GLU* 3.0 14.2 + - - -
320D ALA* 3.3 13.9 - - - -
321D PHE 3.1 0.4 - - - -
322D VAL* 1.3 79.4 - - - +
324D MET* 1.3 62.5 + - - +
326D ASP* 3.5 8.7 + - - +
327D ASN* 3.2 27.4 + - - +
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Residues in contact with MET 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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316D LEU* 3.7 30.1 - - + -
320D ALA* 3.2 19.5 + - + +
321D PHE* 3.1 7.9 + - - +
323D SER* 1.3 77.2 - - - +
325D ILE* 1.3 58.5 + - - +
326D ASP 3.0 4.3 - - - -
327D ASN* 2.9 28.5 + - - +
328D GLY 3.8 3.1 + - - -
342D THR* 3.2 35.4 - - - +
343D LEU* 3.3 34.2 + - + +
346D PHE* 3.7 28.5 - - + -
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Residues in contact with ILE 325 (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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321D PHE* 3.2 23.5 + - + +
322D VAL* 3.3 17.2 + - + +
324D MET* 1.3 75.8 - - - +
326D ASP* 1.3 61.0 + - + +
328D GLY 5.0 0.2 - - - +
329D LYS* 3.1 40.3 + - + +
343D LEU* 3.5 28.5 - - + -
403D VAL 4.3 15.7 - - - +
407D ASP* 3.6 39.0 - - + +
408D ALA* 4.0 9.4 - - + +
411D ALA* 3.5 15.0 - - + -
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Residues in contact with ASP 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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322D VAL* 3.2 16.3 + - + +
323D SER* 3.5 13.0 - - - +
324D MET 3.0 0.4 - - - -
325D ILE* 1.3 81.4 - - + +
327D ASN* 1.3 66.0 + - - +
328D GLY 3.4 0.3 + - - -
329D LYS 4.0 15.4 - - - +
403D VAL* 5.3 10.4 - - - +
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Residues in contact with ASN 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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323D SER* 3.2 21.9 + - - +
324D MET* 2.9 11.0 + - - +
326D ASP* 1.3 80.9 - - - +
328D GLY* 1.3 58.6 + - - +
342D THR* 2.8 37.2 + - - +
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Residues in contact with GLY 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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324D MET 3.8 5.3 + - - -
325D ILE 4.7 0.2 - - - -
326D ASP 4.3 0.4 - - - -
327D ASN* 1.3 79.5 - - - +
329D LYS* 1.3 67.2 + - - +
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Residues in contact with LYS 329 (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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421C ARG* 3.5 9.8 - - - +
325D ILE* 3.1 28.7 + - + +
326D ASP* 4.0 13.6 - - - -
328D GLY* 1.3 83.8 - - - +
407D ASP* 4.7 29.2 - - + +
410D GLU* 2.9 35.3 + - + +
411D ALA* 5.9 4.7 - - + +
414D ASP* 2.3 31.7 + - - -
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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