Contacts of the strand formed by residues 125 - 131 (chain H) 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 H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91H ILE 3.6 0.6 - - - +
92H LEU* 3.4 7.7 - - - +
93H VAL* 3.0 48.4 + - + +
95H VAL* 3.6 25.8 - - + -
100H TYR* 3.4 31.9 - - + +
103H VAL* 4.0 5.2 - - - -
104H ALA* 4.0 15.9 - - + -
107H LEU* 3.7 25.6 - - + -
116H VAL* 4.9 2.0 - - + -
117H TYR 3.0 21.8 - - - +
118H GLU* 4.2 6.7 - - + -
119H THR* 3.6 4.5 + - - -
123H TYR* 3.7 1.2 - - - +
124H ASP* 1.3 85.7 + - + +
126H VAL* 1.3 64.1 + - - +
127H VAL* 4.9 2.2 - - + -
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Residues in contact with VAL 126 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90G PHE* 4.1 28.5 - - + -
156G MET* 4.2 11.7 - - - -
90H PHE* 3.8 32.1 - - + -
91H ILE 3.6 4.3 - - - +
92H LEU* 3.6 24.0 - - + -
116H VAL* 3.7 0.7 - - - -
117H TYR* 2.9 36.2 + - + +
119H THR* 3.8 26.0 + - + +
125H MET* 1.3 74.6 - - - +
127H VAL* 1.3 65.5 + - - +
128H LYS* 6.0 0.2 - - + -
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Residues in contact with VAL 127 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89H ALA 3.8 0.3 - - - +
90H PHE* 3.3 5.4 - - - -
91H ILE* 2.8 57.9 + - + +
93H VAL* 4.5 6.7 - - + -
107H LEU* 3.8 29.2 - - + -
113H ILE* 3.6 34.8 - - + -
115H GLU 3.3 3.6 - - - -
116H VAL* 4.1 18.8 - - + -
125H MET* 4.9 2.2 - - + -
126H VAL* 1.3 82.5 - - - +
128H LYS* 1.3 65.7 + - - +
129H ILE 4.0 0.2 + - - -
144H ILE* 5.4 1.6 - - + -
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Residues in contact with LYS 128 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115G GLU* 2.8 27.7 + - - -
117G TYR* 3.1 16.0 + - - -
88H LEU* 3.6 24.2 - - + -
89H ALA 3.6 5.2 - - - +
90H PHE* 3.6 31.0 - - + -
113H ILE* 3.4 4.0 - - - +
114H VAL* 2.9 42.8 + - + +
115H GLU* 2.9 53.6 + - + +
117H TYR* 5.9 0.4 - - + -
126H VAL* 5.1 0.6 - - + +
127H VAL* 1.3 73.9 - - - +
129H ILE* 1.3 62.0 + - - +
130H ARG* 4.8 6.8 - - - +
164H GLU* 4.6 3.0 + - - +
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Residues in contact with ILE 129 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87H MET* 4.6 0.7 - - + +
88H LEU* 3.6 3.8 - - - +
89H ALA* 3.0 46.0 + - + +
91H ILE* 3.6 30.5 - - + -
112H GLU* 3.6 18.4 - - + +
113H ILE* 4.1 14.8 - - + -
127H VAL* 4.6 0.4 - - + -
128H LYS* 1.3 74.1 - - - +
130H ARG* 1.3 67.0 + - - +
131H THR* 4.0 11.7 - - + -
137H LEU* 3.8 17.7 - - + -
140H PHE* 3.7 44.2 - - + -
144H ILE* 5.0 0.4 - - + -
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Residues in contact with ARG 130 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117G TYR* 4.7 0.6 + - - -
168G LEU* 3.6 30.1 - - + +
169G PRO* 6.2 1.3 - - + -
80H PRO* 3.6 31.9 - - - +
85H TYR* 3.6 26.6 - - + -
87H MET 3.3 9.8 + - - +
88H LEU* 3.8 34.6 - - + +
112H GLU* 3.2 23.6 + - - +
114H VAL* 4.8 17.8 - - + +
128H LYS* 4.8 6.1 - - - +
129H ILE* 1.3 78.1 - - - +
131H THR* 1.3 69.1 + - - +
164H GLU* 2.6 35.8 + - - -
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Residues in contact with THR 131 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85H TYR* 3.4 12.1 - - - -
86H SER 3.1 5.2 + - - -
87H MET* 3.0 45.7 + - - +
112H GLU* 5.0 1.8 - - + -
129H ILE* 4.0 24.0 - - + -
130H ARG* 1.3 79.7 - - - +
132H LYS* 1.3 60.0 + - - +
133H ASN 3.0 22.1 + - - -
136H GLU* 4.2 5.8 - - + -
137H LEU* 3.8 22.8 - - + +
140H PHE* 4.1 14.6 - - + -
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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