Contacts of the helix formed by residues 298 - 305 (chain A) in PDB entry 3F78
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 LEU 298 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1A ICF 3.8 16.8 - - - -
153A PHE* 4.3 9.6 - - + -
259A ILE* 3.6 34.3 - - + -
287A LYS* 4.5 17.3 - - + -
289A LEU* 4.0 30.3 - - + -
294A LYS 4.5 5.4 - - - +
295A LEU* 3.1 15.3 + - + +
297A ASP* 1.3 82.8 - - + +
299A PHE* 1.3 64.4 + - - +
300A THR 3.4 1.3 - - - -
301A GLU* 3.3 23.8 + - - +
302A LEU* 3.0 23.4 + - + +
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Residues in contact with PHE 299 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153A PHE* 3.6 28.9 - + - -
156A ASP* 3.5 36.8 - - + -
157A VAL* 4.0 15.9 - - + -
160A LYS* 3.6 28.9 - - + -
295A LEU 4.7 0.2 - - - -
296A LYS* 3.1 52.3 - - + +
297A ASP 3.5 2.2 - - - -
298A LEU* 1.3 78.1 - - - +
300A THR* 1.3 64.4 + - - +
302A LEU* 3.3 5.1 + - - +
303A GLN* 3.0 40.1 + - - +
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Residues in contact with THR 300 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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296A LYS 5.2 0.2 + - - -
297A ASP 4.8 4.3 + - - -
298A LEU 3.4 0.4 - - - -
299A PHE* 1.3 78.3 - - - +
301A GLU* 1.3 63.5 + - - +
303A GLN* 3.4 9.4 + - - +
304A LYS* 3.2 54.2 + - - +
145C ASP* 4.0 30.8 - - - +
149C LYS* 5.2 3.1 - - - +
293C GLU* 5.1 1.6 - - - +
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Residues in contact with GLU 301 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1A ICF 3.5 9.4 - - + +
284A GLU* 4.3 1.6 - - - +
287A LYS* 2.6 37.5 + - - +
297A ASP 5.2 2.5 + - - +
298A LEU* 3.3 21.8 + - - +
299A PHE 3.2 0.6 - - - -
300A THR* 1.3 77.0 - - - +
302A LEU* 1.3 66.5 + - - +
304A LYS* 3.2 16.5 + - - +
305A LYS* 2.9 41.6 + - - +
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Residues in contact with LEU 302 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1A ICF 3.2 48.4 - - + +
132A LEU* 5.5 3.4 - - + -
153A PHE* 4.5 4.3 - - + -
157A VAL* 3.7 32.5 - - + -
161A LEU* 3.5 31.4 - - + -
166A TYR* 4.2 10.7 + - + +
235A ILE* 3.7 20.2 - - + -
298A LEU 3.0 16.6 + - - +
299A PHE* 3.8 4.7 - - - +
301A GLU* 1.3 75.7 - - - +
303A GLN* 1.3 65.3 + - + +
305A LYS* 3.3 17.3 + - - +
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Residues in contact with GLN 303 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160A LYS* 3.8 39.1 + - + +
161A LEU* 4.2 26.2 - - + +
166A TYR* 5.4 1.6 + - - -
299A PHE* 3.0 37.4 + - - +
300A THR* 3.8 8.7 + - - +
302A LEU* 1.3 80.9 - - + +
304A LYS* 1.3 61.1 + - + +
305A LYS 3.5 4.9 + - - +
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Residues in contact with LYS 304 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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300A THR* 3.2 41.7 + - + +
301A GLU* 3.8 8.1 - - - +
302A LEU 3.2 0.6 - - - -
303A GLN* 1.3 77.5 - - + +
305A LYS* 1.3 66.1 + - - +
306A ILE* 3.4 11.8 + - - +
283B SER* 4.3 6.1 - - - -
145C ASP* 4.3 8.0 + - - -
146C GLU* 5.8 4.1 + - - +
293C GLU* 3.1 31.3 + - - -
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Residues in contact with LYS 305 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1A ICF 3.1 38.8 - - - -
166A TYR* 4.4 8.2 + - - +
257A TYR* 3.6 9.6 - - - +
284A GLU* 2.7 30.4 + - - +
301A GLU* 2.9 40.2 + - - +
302A LEU 3.3 14.7 + - - +
303A GLN 3.3 4.9 - - - +
304A LYS* 1.3 78.9 - - - +
306A ILE* 1.3 62.8 + - - +
307A TYR* 3.7 24.2 + - + +
281B PRO* 4.5 3.1 - - + -
283B SER* 3.6 13.2 + - - +
284B GLU* 6.0 0.2 - - - +
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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