Contacts of the helix formed by residues 320 - 325 (chain F) in PDB entry 1II4
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 THR 320 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63B GLN* 5.6 10.1 - - + +
65B GLN* 3.4 14.6 + - - +
316F GLY 3.3 2.5 + - - -
317F VAL* 4.2 10.6 + - - -
318F ASN 3.8 1.2 + - - -
319F THR* 1.3 77.0 - - - +
321F ASP* 1.3 67.7 + - + +
322F LYS* 3.0 31.0 + - + +
323F GLU* 3.0 27.6 + - - +
324F ILE* 3.3 3.8 + - - +
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Residues in contact with ASP 321 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B PHE* 3.7 20.1 - - + -
27B LYS* 3.7 31.2 + - + +
63B GLN* 4.9 3.0 + - - +
64B LEU 4.1 5.4 - - - +
65B GLN* 3.0 35.1 + - - +
66B ALA 4.9 0.5 + - - -
285F GLN* 3.8 20.3 + - - -
286F PRO 4.5 8.2 - - - +
288F ILE* 4.9 2.1 - - - +
315F ALA* 4.0 9.0 - - - +
319F THR 3.8 0.2 + - - -
320F THR* 1.3 75.7 - - + +
322F LYS* 1.3 63.1 + - - +
323F GLU* 3.0 1.6 + - - -
324F ILE* 3.3 24.9 + - + +
325F GLU* 4.1 6.8 + - - +
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Residues in contact with LYS 322 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B LYS* 4.8 16.8 + - - +
320F THR* 3.0 23.2 - - + +
321F ASP* 1.3 78.3 - - - +
323F GLU* 1.3 60.5 + - + +
325F GLU* 6.0 0.5 - - - +
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Residues in contact with GLU 323 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313F LYS* 2.8 30.5 + - - +
318F ASN 5.3 1.0 - - - +
319F THR* 3.5 23.6 - - - +
320F THR* 3.0 29.5 + - - +
321F ASP 3.1 0.4 - - - -
322F LYS* 1.3 81.4 - - + +
324F ILE* 1.3 64.0 + - - +
325F GLU 3.3 3.3 + - - +
326F VAL* 3.3 19.0 - - + +
328F TYR* 6.0 2.2 - - + -
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Residues in contact with ILE 324 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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288F ILE* 3.7 36.8 - - + +
290F TRP* 2.9 28.8 + - + -
313F LYS* 3.7 34.5 + - + +
314F ALA* 4.0 2.9 - - - +
315F ALA* 3.7 22.0 - - + +
319F THR* 3.8 10.1 - - + +
320F THR 3.6 9.4 - - - +
321F ASP* 3.3 35.6 + - + +
323F GLU* 1.3 79.0 + - - +
325F GLU* 1.3 70.1 + - + +
326F VAL 3.2 2.3 + - - +
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Residues in contact with GLU 325 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25B HIS* 4.5 0.6 + - - -
26B PHE* 3.8 23.8 - - + -
27B LYS* 2.8 30.6 + - - +
277F VAL* 3.6 4.1 - - + +
278F CYS* 2.8 44.5 + - + +
279F LYS* 3.7 17.5 + - + +
280F VAL* 3.1 28.9 + - - +
288F ILE* 4.7 8.1 - - + -
290F TRP* 3.6 7.2 - - - +
321F ASP 4.1 6.0 + - - +
322F LYS 6.0 0.4 - - - +
323F GLU* 3.3 1.4 - - - -
324F ILE* 1.3 87.3 - - + +
326F VAL* 1.3 59.6 + - + +
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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