Contacts of the helix formed by residues 323 - 333 (chain D) in PDB entry 4HHM
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 323 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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319D ALA 3.0 17.5 + - - +
320D PHE 3.2 1.8 + - - -
321D ARG 3.3 0.2 - - - -
322D ALA* 1.3 75.1 - - - +
324D PRO* 1.3 67.7 - - - +
325D GLU* 2.6 33.3 + - - +
326D VAL* 2.8 39.7 + - + +
327D GLN* 2.8 14.8 + - - +
382D HIS* 3.0 19.9 + - + +
387D ARG* 2.9 26.9 + - - -
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Residues in contact with PRO 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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322D ALA 3.3 9.6 - - - +
323D ASP* 1.3 88.5 - - - +
325D GLU* 1.3 56.7 + - - +
327D GLN* 3.4 14.5 + - + +
328D GLU* 3.0 29.3 + - - +
331D ARG* 5.3 0.9 + - - -
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Residues in contact with GLU 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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323D ASP* 2.6 17.4 + - - +
324D PRO* 1.3 75.4 - - - +
326D VAL* 1.3 56.3 + - - +
328D GLU* 3.4 20.5 + - - +
329D ALA* 3.0 26.5 + - - +
374D ARG* 6.1 1.4 - - - +
378D LEU* 3.9 18.7 - - + +
387D ARG* 3.3 28.8 + - - +
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Residues in contact with VAL 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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320D PHE* 3.1 66.4 - - + +
321D ARG* 4.7 1.3 - - - +
323D ASP* 2.8 19.0 + - + +
325D GLU* 1.3 75.7 - - - +
327D GLN* 1.3 52.7 + - - +
329D ALA* 2.9 5.0 + - - +
330D LEU* 2.8 47.3 + - + +
375D LEU* 4.6 2.7 - - + -
378D LEU* 3.9 19.7 - - + -
382D HIS* 3.6 17.3 - - + +
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Residues in contact with GLN 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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321D ARG 3.0 28.1 - - - +
322D ALA* 3.6 15.3 - - - +
323D ASP 2.8 19.4 + - - +
324D PRO* 3.8 11.3 - - - +
326D VAL* 1.3 72.7 - - - +
328D GLU* 1.3 61.9 + - - +
330D LEU* 3.2 19.6 + - + +
331D ARG* 3.2 39.8 + - - +
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Residues in contact with GLU 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 PRO 3.0 17.3 + - - +
325D GLU* 3.5 23.3 - - - +
326D VAL 3.1 0.2 - - - -
327D GLN* 1.3 76.1 - - - +
329D ALA* 1.3 63.4 + - - +
331D ARG* 3.3 25.8 + - - +
332D ALA* 3.1 20.8 + - + +
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Residues in contact with ALA 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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325D GLU 3.0 12.7 + - - +
326D VAL 2.9 9.7 + - - +
328D GLU* 1.3 77.2 - - - +
330D LEU* 1.3 60.9 - - - +
332D ALA* 3.3 10.0 + - - +
333D ALA* 3.1 23.4 + - - +
371D ALA 5.0 1.8 - - - +
374D ARG* 6.0 4.3 - - + -
375D LEU* 3.9 22.2 - - + +
378D LEU* 3.6 21.5 - - + -
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Residues in contact with LEU 330 (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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147C ALA* 4.7 5.4 - - + -
320D PHE* 4.9 0.7 - - + -
321D ARG* 4.0 33.4 - - - +
326D VAL* 2.8 23.6 + - + +
327D GLN* 3.3 28.9 - - + +
329D ALA* 1.3 78.0 - - - +
331D ARG* 1.3 62.5 + - + +
333D ALA 3.2 6.8 + - - -
335D LEU* 3.1 45.0 + - + +
336D ASP* 5.1 0.9 - - - -
375D LEU* 3.7 28.3 - - + -
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Residues in contact with ARG 331 (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 PRO 5.3 0.4 + - - -
327D GLN* 3.2 28.8 + - - +
328D GLU* 3.6 30.8 - - - +
330D LEU* 1.3 78.8 - - + +
332D ALA* 1.3 61.3 + - - +
334D ARG* 3.0 22.5 + - - +
336D ASP* 3.7 29.7 - - + +
368D ARG* 5.3 0.5 + - - -
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Residues in contact with ALA 332 (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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328D GLU* 3.1 15.1 + - + +
329D ALA* 3.5 15.3 - - - +
330D LEU 3.2 0.2 - - - -
331D ARG* 1.3 78.7 - - - +
333D ALA* 1.3 55.7 + - - +
334D ARG* 3.0 24.9 + - - -
368D ARG* 3.9 7.9 + - - +
370D MET 4.0 2.0 - - - +
371D ALA* 4.3 14.6 - - + +
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Residues in contact with ALA 333 (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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107C ASN* 3.5 14.4 + - - +
329D ALA 3.1 13.6 + - - +
331D ARG 3.2 0.6 - - - -
332D ALA* 1.3 75.4 - - - +
334D ARG* 1.3 72.6 + - - +
335D LEU* 3.0 27.3 + - + +
370D MET* 3.2 24.1 - - - +
371D ALA 4.3 6.1 - - - +
372D PHE* 3.7 13.7 - - + -
375D LEU* 4.3 4.9 - - + -
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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