Contacts of the helix formed by residues 497 - 502 (chain A) in PDB entry 1U1H
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 VAL 497 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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495A ASP* 3.2 8.7 + - - +
496A MSE 1.3 79.3 - - + +
498A GLU* 1.3 68.4 + - - +
499A TYR 3.2 1.3 - - - -
500A PHE* 3.0 7.6 + - - +
501A GLY* 2.9 17.8 + - - -
507A PHE* 4.9 2.7 - - + -
526A PRO* 4.1 22.7 - - + -
559A THR* 4.7 0.7 - - + -
563A THR* 4.3 9.0 - - + +
564A ILE* 4.1 46.9 - - + +
567A TRP* 4.2 32.5 - - + +
568A SER* 4.2 7.2 - - - +
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Residues in contact with GLU 498 (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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495A ASP* 3.0 32.6 + - + +
497A VAL* 1.3 75.8 - - - +
499A TYR* 1.3 64.6 + - - +
501A GLY 4.2 0.4 - - - +
502A GLU* 2.9 42.8 + - + +
509A PHE* 3.3 36.6 - - + +
524A LYS* 3.9 28.1 + - - +
526A PRO* 3.7 11.2 - - + -
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Residues in contact with TYR 499 (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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492A GLU* 3.7 34.4 + - + -
493A ARG* 3.5 45.7 + - + -
494A ASN 5.0 1.1 - - - +
495A ASP* 3.0 23.4 + - - +
496A MSE 4.4 3.1 - - - +
498A GLU* 1.3 77.9 - - - +
500A PHE* 1.3 83.1 + + - +
502A GLU* 4.2 14.5 + - - +
503A GLN* 3.3 41.2 + - - +
538A MSE 3.2 20.1 + - - -
539A THR* 4.2 6.5 + - - -
542A TRP* 3.7 14.3 + - - -
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Residues in contact with PHE 500 (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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493A ARG* 3.6 16.2 - - - -
496A MSE 3.0 23.8 - - - -
497A VAL 3.0 5.8 + - - +
499A TYR* 1.3 93.8 - + + +
501A GLY* 1.3 66.3 + - - +
502A GLU 3.2 1.8 - - - -
503A GLN* 3.0 13.0 + - - +
504A LEU* 3.1 22.5 + - + +
538A MSE 3.7 29.7 - - + +
539A THR* 3.6 20.2 - - - -
557A MSE 3.5 21.5 - - - -
558A LEU* 3.7 17.9 - - + -
559A THR* 3.3 29.8 - - - -
564A ILE* 4.3 16.4 - - + -
587A ILE* 5.3 3.8 - - + -
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Residues in contact with GLY 501 (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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497A VAL 2.9 13.6 + - - -
498A GLU* 3.1 0.8 + - - -
500A PHE* 1.3 76.8 - - - +
502A GLU* 1.3 60.8 + - - +
503A GLN 3.1 0.9 + - - -
504A LEU* 3.1 13.0 + - - +
507A PHE* 3.4 49.5 - - - +
509A PHE* 3.4 13.0 - - - -
564A ILE* 5.8 0.4 - - - +
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Residues in contact with GLU 502 (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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498A GLU* 2.9 38.4 + - - +
499A TYR* 4.3 15.8 - - - +
500A PHE 3.2 0.2 - - - -
501A GLY* 1.3 76.6 - - - +
503A GLN* 1.3 62.5 + - + +
504A LEU 3.5 2.1 + - - +
509A PHE* 3.7 23.8 - - + -
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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