Contacts of the helix formed by residues 320 - 324 (chain D) in PDB entry 4OGB
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 SER 320 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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102D TRP* 3.8 25.4 - - - -
167D ASP* 4.2 6.2 + - - -
171D SER* 3.6 13.0 + - - -
316D CYS 3.4 9.0 - - - -
317D ALA* 2.7 25.6 + - - -
318D ASP 3.3 1.8 + - - -
319D LEU* 1.3 75.0 - - - +
321D ASN* 1.3 67.1 + - - +
322D PRO* 3.3 4.0 - - - -
323D THR* 2.6 26.4 + - - -
324D LYS* 3.5 12.6 + - - +
381D TRP* 4.0 4.3 - - - +
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Residues in contact with ASN 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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159D TYR* 2.5 41.3 + - - -
164D HIS* 5.1 1.8 + - - -
167D ASP* 3.4 23.2 + - - -
318D ASP 5.0 3.5 + - - -
319D LEU 3.5 0.4 - - - -
320D SER* 1.3 78.9 + - - +
322D PRO* 1.4 68.5 - - + +
323D THR 3.2 1.2 + - - -
324D LYS* 3.3 19.4 + - - +
329D TYR* 3.4 24.2 - - + +
332D TRP* 3.4 35.7 - - + +
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Residues in contact with PRO 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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319D LEU* 3.7 13.0 - - - +
320D SER 3.4 4.5 - - - -
321D ASN* 1.4 93.2 - - + +
323D THR* 1.3 55.2 + - - +
324D LYS 3.4 0.7 - - - -
329D TYR* 3.5 39.0 - - + +
372D PHE* 4.6 12.6 - - + -
373D ILE* 4.1 4.5 - - + -
377D VAL* 4.0 19.5 - - + -
399D LEU* 3.4 32.6 - - + +
402D ASN* 2.9 23.1 + - - +
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Residues in contact with THR 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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102D TRP* 3.1 35.7 + - - -
320D SER* 2.6 19.7 + - - +
322D PRO* 1.3 79.0 - - - +
324D LYS* 1.3 60.4 + - - +
325D PRO* 4.5 0.3 - - - +
377D VAL* 4.6 2.0 - - + -
381D TRP* 3.7 38.4 - - + +
395D ILE* 3.4 24.9 - - + +
398D THR* 3.3 19.5 - - - +
399D LEU* 4.2 18.8 - - + +
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Residues in contact with LYS 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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102D TRP* 3.3 46.9 - - + +
103D GLY* 4.0 16.9 - - - +
104D LEU 6.0 0.2 - - - +
167D ASP* 3.0 20.6 + - - -
170D GLN* 4.6 6.2 + - - -
171D SER* 2.8 24.6 + - - -
320D SER* 3.5 18.9 + - - +
321D ASN* 3.3 16.0 + - - +
323D THR* 1.3 79.5 - - - +
325D PRO* 1.3 78.6 - - + +
326D LEU* 4.0 0.3 - - - -
328D LEU* 4.1 16.6 - - + -
329D TYR* 4.2 1.8 - - - +
332D TRP* 5.2 5.8 - - + +
398D THR* 3.6 2.5 - - - +
402D ASN* 2.8 21.8 + - - -
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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