Contacts of the strand formed by residues 55 - 58 (chain A) in PDB entry 1U4E
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 55 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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46A PHE* 2.8 47.1 - - + -
53A CYS* 3.2 6.1 + - + +
54A ASN* 1.3 78.5 - - - +
56A GLN* 1.3 69.5 + - - +
57A HIS* 3.8 25.9 + - + +
265A VAL* 4.0 17.7 - - + -
266A SER* 4.4 5.6 - - - -
338A PHE* 3.3 7.2 - - + +
340A VAL* 3.6 28.7 - - + -
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Residues in contact with GLN 56 (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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54A ASN 5.4 0.2 - - - -
55A VAL* 1.3 78.7 - - - +
57A HIS* 1.3 65.5 + - - +
58A GLY 3.7 0.2 + - - -
337A PHE* 3.3 58.7 - - + +
338A PHE 2.7 11.0 + - - +
339A LYS* 3.4 7.1 - - + +
340A VAL* 2.8 31.2 + - - +
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Residues in contact with HIS 57 (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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55A VAL* 3.8 24.5 + - + +
56A GLN* 1.3 78.3 - - - +
58A GLY* 1.3 57.4 + - - +
60A LEU* 3.1 19.2 - - + +
217A ASN 3.8 11.9 - - - -
218A LEU* 3.8 12.4 - - + +
219A ARG 5.8 1.3 - - - -
220A ASN* 4.4 20.3 + - - -
265A VAL* 3.4 32.6 + - + +
340A VAL* 4.6 1.9 - - + +
342A TYR* 2.7 35.1 + - + -
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Residues in contact with GLY 58 (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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56A GLN 3.7 2.0 + - - -
57A HIS* 1.3 72.5 - - - +
59A ASN* 1.4 65.5 + - - +
60A LEU* 3.2 5.3 - - - +
339A LYS* 4.6 15.1 - - - +
340A VAL 2.7 18.6 + - - +
341A ASP* 4.6 0.7 - - - -
342A TYR* 2.9 31.6 + - - -
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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