Contacts of the strand formed by residues 104 - 114 (chain C) in PDB entry 4ZIN
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 VAL 104 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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96C VAL* 5.1 4.0 - - + -
97C MET 3.4 7.6 - - - +
98C ASN* 3.5 18.6 - - - +
102C GLY 3.5 10.8 - - - +
103C GLY* 1.3 79.5 - - - +
105C VAL* 1.3 75.4 + - - +
106C THR* 4.2 14.6 - - + +
125C ARG 3.5 1.8 - - - +
126C GLY* 3.1 4.3 - - - -
127C THR* 2.9 50.1 + - - +
128C ASN* 5.2 2.5 - - + -
129C PHE* 4.0 1.7 - - - -
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Residues in contact with VAL 105 (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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60C ILE* 4.4 14.6 - - + +
64C GLN* 4.5 0.7 - - - +
95C ARG 3.9 0.2 - - - +
96C VAL* 3.5 1.9 - - - -
97C MET* 2.7 58.3 + - + +
99C PHE* 3.9 8.7 - - + -
104C VAL* 1.3 80.1 - - - +
106C THR* 1.3 65.4 + - - +
107C VAL* 3.7 23.1 - - + -
124C LEU* 3.8 23.6 - - + -
125C ARG 3.3 3.1 - - - +
126C GLY* 3.9 9.2 - - - -
129C PHE* 3.9 21.3 - - + -
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Residues in contact with THR 106 (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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95C ARG 3.3 5.6 - - - -
96C VAL* 4.3 20.4 - - + -
104C VAL* 4.2 15.3 - - + -
105C VAL* 1.3 78.0 - - - +
107C VAL* 1.3 66.1 + - - +
108C THR* 6.3 0.4 - - - -
124C LEU* 3.4 2.6 - - - -
125C ARG* 2.9 53.2 + - - +
302C SO4 2.8 25.1 + - - -
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Residues in contact with VAL 107 (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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64C GLN* 3.7 23.1 - - + +
93C TRP* 3.5 27.3 - - + -
94C GLU* 3.4 2.9 - - - +
95C ARG* 2.8 43.9 + - + +
97C MET* 5.0 0.2 - - - -
105C VAL* 3.7 20.0 - - + -
106C THR* 1.3 83.7 - - - +
108C THR* 1.3 70.6 + - - +
122C VAL* 3.6 21.8 - - + -
123C LYS 3.3 12.1 - - - +
124C LEU* 4.3 4.0 - - + -
302C SO4 3.8 0.7 - - - -
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Residues in contact with THR 108 (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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93C TRP 3.3 9.0 - - - +
94C GLU* 4.6 15.5 - - + -
106C THR* 6.3 0.2 - - - -
107C VAL* 1.3 81.2 - - - +
109C GLN* 1.3 61.4 + - - +
121C LYS 3.8 0.5 - - - +
122C VAL* 3.3 4.9 - - - +
123C LYS* 2.9 50.7 + - - +
302C SO4 3.1 26.3 + - - +
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Residues in contact with GLN 109 (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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64C GLN 5.2 0.6 + - - -
66C CH6 3.7 11.5 + - - -
91C PHE* 4.3 0.9 - - - +
92C LYS* 3.1 7.8 - - - +
93C TRP* 2.8 77.2 + - + +
108C THR* 1.3 75.9 - - - +
110C ASP* 1.3 69.5 + - - +
111C SER* 2.5 31.0 + - - -
120C TYR* 3.3 33.1 - - - +
121C LYS 3.2 10.3 - - - +
122C VAL* 3.8 13.9 - - + +
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Residues in contact with ASP 110 (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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91C PHE 3.9 2.9 - - - -
92C LYS* 3.5 25.9 + - + +
109C GLN* 1.3 80.1 - - - +
111C SER* 1.3 65.8 + - - +
112C SER* 4.0 6.1 + - - -
119C ILE 3.5 1.7 - - - +
120C TYR* 3.3 4.7 - - - -
121C LYS* 2.9 54.6 + - + +
184C LYS* 3.3 29.2 + - - -
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Residues in contact with SER 111 (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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66C CH6 5.0 0.3 + - - -
87C PHE* 4.2 4.7 - - - -
90C GLY* 3.4 2.1 - - - -
91C PHE* 3.0 63.4 + - - +
109C GLN* 2.5 31.2 + - - -
110C ASP* 1.3 75.4 + - - +
112C SER* 1.3 61.0 + - - +
119C ILE 3.4 4.5 - - - -
120C TYR* 3.5 13.8 - - - -
184C LYS* 3.3 7.8 + - - -
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Residues in contact with SER 112 (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 PHE* 3.9 7.0 - - - -
88C PRO 4.6 0.7 - - - -
89C GLU 4.0 14.6 - - - -
110C ASP* 4.0 5.1 + - - -
111C SER* 1.3 74.5 - - - +
113C LEU* 1.3 63.7 + - - +
114C GLN* 5.0 6.9 - - - +
118C PHE* 3.3 9.2 - - - +
119C ILE* 2.8 47.4 + - - +
184C LYS* 4.0 7.4 - - - -
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Residues in contact with LEU 113 (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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7C ILE* 3.9 29.6 - - + +
8C ILE* 5.3 0.9 - - + -
12C MET* 3.4 22.9 - - + -
87C PHE* 3.9 16.2 - - + -
88C PRO* 3.2 45.2 + - + +
112C SER* 1.3 77.4 - - - +
114C GLN* 1.3 75.8 + - - +
116C GLY* 3.9 6.5 - - - +
117C GLU 3.2 37.9 - - - +
118C PHE* 3.9 8.7 - - + -
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Residues in contact with GLN 114 (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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112C SER* 4.2 9.8 - - - +
113C LEU* 1.3 83.4 - - - +
115C ASP* 1.3 83.4 + - + +
116C GLY 3.1 2.2 - - - -
117C GLU* 3.0 22.7 + - - +
119C ILE* 4.6 15.2 - - + +
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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