Contacts of the strand formed by residues 157 - 159 (chain C) in PDB entry 3ZXT
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 157 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74C PRO 4.0 2.1 - - - +
75C ASN* 3.2 32.4 - - - +
101C LEU* 4.4 7.4 - - + -
119C PHE* 4.1 25.8 - - + +
122C GLN* 2.8 53.3 - - + +
123C ILE* 4.0 18.4 - - + +
145C ILE* 4.5 12.1 - - + -
146C MET 3.2 9.6 - - - +
147C LEU* 3.6 20.0 - - + -
156C ARG* 1.3 75.1 - - - +
158C LYS* 1.3 65.4 + - - +
159C ILE* 4.1 13.7 - - + +
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Residues in contact with LYS 158 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73C HIS 3.8 2.6 + - - -
74C PRO* 2.9 31.6 + - - +
75C ASN 3.6 1.1 - - - -
76C VAL 2.9 27.5 + - - +
77C ILE* 4.3 1.3 - - - +
78C THR* 5.6 1.2 - - - -
94C GLU* 3.1 36.9 + - - +
96C VAL* 3.7 35.2 - - + -
145C ILE* 5.2 0.2 - - - -
146C MET* 3.1 32.3 + - - +
148C LEU* 4.4 24.9 - - + -
156C ARG* 3.8 1.9 + - - -
157C ILE* 1.3 77.3 - - - +
159C ILE* 1.3 63.6 + - - +
160C ILE* 3.5 5.4 + - + +
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Residues in contact with ILE 159 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75C ASN 2.8 25.9 + - - +
76C VAL* 3.6 10.3 - - + -
77C ILE* 3.0 25.8 + - - +
123C ILE* 4.2 13.2 - - + +
126C GLY* 3.8 28.0 - - - -
127C VAL* 4.3 8.7 - - + -
130C LEU* 4.8 4.3 - - + -
137C HIS* 3.5 33.2 - - + +
140C LEU* 3.8 13.0 - - + -
144C ASN 4.0 6.7 - - - +
145C ILE* 4.4 13.9 - - + -
157C ILE* 4.1 14.8 - - + -
158C LYS* 1.3 71.5 - - - +
160C ILE* 1.3 61.8 + - - +
162C PHE* 3.7 7.7 - - + -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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