Contacts of the strand formed by residues 121 - 124 (chain O) in PDB entry 5KZ5
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 ILE 121 (chain O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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117F PRO* 5.0 2.0 - - + -
119O ARG* 4.4 4.2 - - - +
120O GLU* 1.3 89.9 + - + +
122O ILE* 1.3 69.9 + - - +
123O PHE 3.3 20.7 + - - +
124O THR* 4.1 7.9 - - + -
129O GLU* 4.8 3.1 - - + +
130O SER* 3.8 34.3 - - - +
133O ILE* 4.3 7.0 - - + -
268O ILE* 3.5 34.8 - - + +
281O LEU* 3.8 41.1 - - + -
282O GLN* 4.8 5.6 - - + +
105R ARG* 5.5 0.4 - - - +
108R GLN* 4.7 10.3 - - - +
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Residues in contact with ILE 122 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115F ASP* 6.0 0.4 - - - +
117F PRO* 3.4 15.9 - - - +
107O ARG* 6.3 1.3 - - - +
119O ARG* 3.7 35.4 - - + +
121O ILE* 1.3 77.0 - - - +
123O PHE* 1.4 75.8 + - + +
282O GLN* 4.0 30.4 - - + +
283O SER 6.2 0.7 - - - -
289O ARG* 3.4 47.3 - - + +
291O MET* 3.7 26.5 - - + +
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Residues in contact with PHE 123 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115F ASP* 4.6 6.1 - - - -
116F LYS* 3.6 50.5 - - + -
117F PRO* 3.8 7.8 - - - +
107O ARG* 3.7 30.3 - - - -
121O ILE* 3.3 19.4 + - - +
122O ILE* 1.4 85.8 - - + +
124O THR* 1.3 71.3 + - - +
129O GLU* 4.5 0.2 - - - +
265O VAL* 3.8 17.9 - - + -
266O GLY 3.4 16.4 - - - +
267O ALA* 4.1 17.0 - - + -
268O ILE* 4.8 1.2 - - - +
289O ARG* 3.8 29.2 - - - -
298O THR* 5.6 4.0 - - + -
299O PRO* 6.5 0.7 - - + -
304O LEU* 5.8 1.3 - - + -
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Residues in contact with THR 124 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116F LYS* 4.4 0.2 - - - +
117F PRO 3.1 9.5 - - - +
121O ILE* 4.1 5.2 - - + -
123O PHE* 1.3 82.1 - - - +
125O SER* 1.3 59.9 + - - +
126O GLY 3.9 7.4 - - - -
129O GLU* 3.3 20.4 - - - +
130O SER* 3.4 18.2 - - - +
254O ILE 3.3 16.1 + - - +
255O SER* 3.5 6.2 + - - -
264O GLY 3.1 17.2 - - - +
265O VAL* 3.3 10.6 - - - -
266O GLY* 3.2 17.8 + - - +
268O ILE* 3.9 21.5 - - + -
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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