Contacts of the strand formed by residues 125 - 131 (chain C) in PDB entry 2ZNZ
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 MET 125 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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91C ILE 3.5 0.6 - - - +
92C LEU* 3.4 8.1 - - - +
93C VAL* 3.0 38.3 + - + -
95C VAL* 4.1 18.4 - - + -
100C TYR* 3.1 34.1 - - + +
103C VAL* 3.8 20.0 - - + -
104C ALA* 3.7 20.4 - - + +
107C LEU* 3.9 14.6 - - - -
116C VAL* 4.7 4.7 - - - -
117C TYR 3.0 14.4 - - - +
118C GLU* 4.0 16.2 - - + -
119C THR* 3.8 2.2 - - - -
123C TYR* 3.7 1.1 - - - +
124C ASP* 1.3 86.3 + - + +
126C VAL* 1.3 67.7 + - - +
127C VAL* 4.8 2.9 - - + -
162D HIS* 4.8 0.4 - - + +
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Residues in contact with VAL 126 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90C PHE* 3.8 30.1 - - + -
91C ILE 3.8 2.0 - - - -
92C LEU* 4.0 12.8 - - + -
115C GLU 3.8 0.3 - - - +
116C VAL* 3.5 2.6 - - - -
117C TYR* 2.9 38.2 + - + +
119C THR* 3.4 32.7 + - + +
125C MET* 1.3 73.2 - - - +
127C VAL* 1.3 65.3 + - - +
128C LYS 4.2 0.4 - - - +
90D PHE* 4.1 28.7 - - + -
156D MET* 3.8 18.8 - - + -
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Residues in contact with VAL 127 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89C ALA 3.6 0.2 - - - +
90C PHE* 3.3 6.9 - - - -
91C ILE* 2.8 58.2 + - + +
93C VAL* 4.2 10.1 - - + -
107C LEU* 3.8 30.5 - - + -
113C ILE* 3.6 38.1 - - + -
115C GLU 3.2 5.4 - - - +
116C VAL* 4.4 9.0 - - + -
125C MET* 4.8 3.1 - - + -
126C VAL* 1.3 80.7 - - - +
128C LYS* 1.3 65.6 + - - +
129C ILE* 4.0 0.6 + - + -
144C ILE* 5.4 0.4 - - + -
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Residues in contact with LYS 128 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88C LEU* 3.6 24.7 - - + -
89C ALA 3.5 5.6 - - - +
90C PHE* 3.7 25.6 - - + -
113C ILE* 3.5 3.8 - - - -
114C VAL* 2.8 42.3 + - + -
115C GLU* 2.9 54.7 + - + +
117C TYR* 6.0 0.2 - - - -
126C VAL* 4.2 0.8 - - - +
127C VAL* 1.3 72.3 - - - +
129C ILE* 1.3 62.5 + - - +
130C ARG* 4.8 6.4 - - - +
164C GLU* 4.6 3.0 + - - +
115D GLU* 2.8 31.6 + - - -
117D TYR* 3.1 20.7 + - - -
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Residues in contact with ILE 129 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87C MET* 4.0 0.7 - - - +
88C LEU* 3.6 4.5 - - - +
89C ALA* 2.9 47.2 + - + +
91C ILE* 3.6 33.0 - - + -
112C GLU* 3.5 15.7 - - + +
113C ILE* 3.9 20.9 - - + -
127C VAL* 4.6 0.7 - - + -
128C LYS* 1.3 75.7 - - - +
130C ARG* 1.3 66.9 + - - +
131C THR* 4.1 13.2 - - + +
137C LEU* 3.7 18.4 - - + -
140C PHE* 3.9 34.8 - - + -
144C ILE* 4.6 2.0 - - + -
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Residues in contact with ARG 130 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80C PRO* 3.7 30.3 - - - +
85C TYR* 3.7 21.4 + - + -
87C MET 3.3 7.7 + - - +
88C LEU* 3.7 34.7 - - + +
112C GLU* 3.1 37.5 + - - +
114C VAL* 5.0 18.3 - - + +
128C LYS* 4.8 5.3 - - - +
129C ILE* 1.3 77.9 - - - +
131C THR* 1.3 62.6 + - - +
164C GLU* 2.7 36.0 + - - -
117D TYR* 4.7 0.4 + - - -
168D LEU* 3.6 30.0 - - + +
169D PRO* 5.8 3.4 - - + -
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Residues in contact with THR 131 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85C TYR* 3.5 12.8 - - - -
86C SER 3.5 4.7 + - - -
87C MET* 3.0 41.4 + - - +
112C GLU* 5.3 0.9 - - - -
129C ILE* 4.1 16.8 - - + -
130C ARG* 1.3 80.3 - - - +
132C LYS* 1.3 64.3 + - - +
133C ASN 2.9 21.6 + - - -
136C GLU* 4.0 4.3 - - - -
137C LEU* 3.7 30.3 - - + +
140C PHE* 4.1 17.0 - - + -
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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