Contacts of the helix formed by residues 97 - 99 (chain S) in PDB entry 1XU1
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 PRO 97 (chain S).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166B THR* 4.3 8.0 - - + +
167B PHE* 4.3 8.5 - - + -
222B ARG* 4.1 28.7 - - + +
78S PHE* 3.8 21.1 - - + -
92S ILE* 3.5 20.2 - - + -
95S GLN 4.3 2.2 - - - +
96S HIS* 1.3 99.6 - - + +
98S LYS* 1.3 67.0 - - - +
99S GLN* 3.5 18.6 - - - +
100S CYS* 3.1 16.7 + - - -
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Residues in contact with LYS 98 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120B ALA* 3.2 27.8 + - - +
121B ASP* 5.0 5.9 + - - +
122B SER 4.0 13.7 - - - +
123B ASP* 4.3 7.6 - - - +
223B ALA* 3.9 28.6 + - + +
224B ASN* 4.4 10.5 - - - +
96S HIS* 5.6 0.2 - - - -
97S PRO* 1.3 73.8 - - - +
99S GLN* 1.3 63.8 + - - +
101S ALA* 3.1 26.8 + - + +
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Residues in contact with GLN 99 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123B ASP* 3.5 42.8 + - - +
221B PRO 4.6 8.3 + - - -
222B ARG* 5.3 5.7 + - - +
223B ALA 5.6 0.3 + - - -
73S LYS* 6.4 2.7 - - - -
78S PHE* 3.7 46.8 - - + +
79S TYR 4.3 8.1 + - - -
80S ASP* 5.3 1.6 - - - +
81S HIS* 5.2 6.1 + - - +
89S CYS* 4.6 2.5 - - - -
97S PRO* 3.2 20.5 + - - +
98S LYS* 1.3 78.1 + - - +
100S CYS* 1.3 59.4 + - - +
101S ALA 3.7 0.3 + - - -
102S TYR* 5.1 1.9 + - - +
103S PHE* 5.8 0.5 - - - +
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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