Contacts of the helix formed by residues 301 - 305 (chain A) in PDB entry 5L0U
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 PHE 301 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57A TYR* 3.4 33.3 - - + +
166A PHE* 4.0 14.6 - + - -
280A PHE* 4.3 3.8 - + - -
281A LYS* 3.9 26.2 - - + -
299A GLU* 3.8 29.6 - - + -
300A PHE* 1.3 97.8 - + + +
302A TYR* 1.3 90.8 + + - +
303A PRO 3.4 2.0 - - - -
304A GLN* 3.3 18.3 + - - +
305A LEU* 3.8 25.6 + - + +
345A PHE* 4.9 1.0 - + - -
346A ILE* 4.5 5.2 - - + -
350A LEU* 3.9 24.2 - - + -
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Residues in contact with TYR 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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270A ASN* 5.0 1.2 + - - -
276A ALA* 3.5 10.4 - - + +
277A SER 3.3 15.6 + - - -
280A PHE* 3.3 37.0 - + + +
292A HIS* 4.4 15.9 - + - -
297A TRP 3.5 26.0 - - - -
298A LEU* 3.6 18.4 - - + -
299A GLU* 2.7 58.3 + - + +
301A PHE* 1.3 93.9 - + - +
303A PRO* 1.3 64.0 - - + +
305A LEU* 2.9 35.4 + - - +
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Residues in contact with PRO 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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60A VAL* 3.9 24.9 - - + -
160A MET* 5.2 1.3 - - + -
298A LEU* 4.6 19.9 - - + -
299A GLU 3.6 5.8 - - - +
300A PHE* 3.4 14.8 - - - +
301A PHE 3.5 1.1 - - - -
302A TYR* 1.3 92.6 - - + +
304A GLN* 1.3 57.7 + - + +
305A LEU 4.1 0.6 - - - +
306A LYS* 2.6 36.5 + - - +
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Residues in contact with GLN 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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46A TYR* 4.4 6.2 + - - -
47A GLU 5.3 3.5 - - - +
49A CYS* 4.1 12.8 + - - +
56A CYS* 3.1 38.2 + - + +
57A TYR* 3.6 20.6 - - + -
60A VAL* 6.0 1.3 - - + -
301A PHE 3.3 7.7 + - - +
302A TYR 3.0 1.4 + - - -
303A PRO* 1.3 82.9 + - + +
305A LEU* 1.3 61.9 + - - +
306A LYS* 3.7 14.8 + - - +
310A HIS* 3.5 17.0 - - - -
345A PHE* 3.4 27.7 - - + -
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Residues in contact with LEU 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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280A PHE* 3.7 27.6 - - + -
284A PHE* 4.1 19.5 - - + -
301A PHE* 3.9 31.6 - - + +
302A TYR* 2.9 18.5 + - + +
303A PRO 4.1 0.5 - - - +
304A GLN* 1.3 76.0 - - - +
306A LYS* 1.3 63.7 + - - +
307A PRO* 4.1 1.4 - - - +
310A HIS* 3.5 23.3 - - + +
311A TYR* 3.7 25.1 + - + -
342A GLY 4.9 0.4 - - - +
345A PHE* 3.6 30.3 - - + -
346A ILE* 4.2 8.1 - - + -
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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