Contacts of the strand formed by residues 120 - 127 (chain F) in PDB entry 4ZZ7
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 GLY 120 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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118F LEU 3.3 3.4 + - - -
119F LYS* 1.3 76.1 - - - +
121F GLU* 1.3 61.5 + - - +
134F SER* 3.4 21.3 - - - -
135F GLU* 5.2 1.1 - - - +
136F PHE* 4.1 12.1 - - - -
120G GLY 3.9 0.2 - - - +
121G GLU* 3.5 7.1 - - - +
122G HIS* 2.7 36.9 + - - -
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Residues in contact with GLU 121 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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447E HIS* 3.6 14.6 + - + -
465E PRO* 4.0 15.2 - - - +
119F LYS 5.6 0.7 - - - +
120F GLY* 1.3 75.0 - - - +
122F HIS* 1.3 59.8 + - - +
133F TRP* 3.2 4.9 - - - -
134F SER* 2.7 40.5 + - - +
136F PHE* 5.9 5.4 - - + -
474F ARG* 4.7 6.8 + - - -
116G GLU* 4.7 4.3 - - - +
119G LYS* 3.1 47.3 + - + +
120G GLY 3.5 7.6 - - - +
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Residues in contact with HIS 122 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120F GLY 4.0 0.8 + - - -
121F GLU* 1.3 73.2 - - - +
123F SER* 1.3 75.8 + - - +
124F ARG* 4.3 1.5 + - + -
131F ASP* 4.5 12.1 + - + -
132F SER 4.9 0.2 - - - -
133F TRP* 3.8 28.9 - + - +
118G LEU 4.3 0.7 - - - +
119G LYS* 3.4 5.7 - - - -
120G GLY* 2.7 45.2 + - - +
122G HIS* 3.7 23.0 + - + -
133G TRP* 3.3 47.7 + + + -
134G SER 4.4 2.5 - - - +
135G GLU* 3.2 29.3 + - + -
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Residues in contact with SER 123 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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446E TYR* 3.7 13.8 - - - -
447E HIS* 3.0 25.8 + - - -
122F HIS* 1.3 80.2 + - - +
124F ARG* 1.3 62.6 + - - +
126F VAL* 3.8 18.2 - - - +
131F ASP* 3.5 5.7 - - - +
132F SER 2.8 38.2 + - - +
115G PRO 4.8 1.5 + - - -
118G LEU 5.4 1.1 - - - -
119G LYS* 3.9 14.0 - - - +
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Residues in contact with ARG 124 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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446E TYR* 5.2 1.2 + - - -
122F HIS* 4.3 3.1 + - + -
123F SER* 1.3 73.0 - - - +
125F ASN* 1.3 95.4 + - - +
126F VAL* 3.6 0.5 + - - -
131F ASP* 4.2 5.2 - - - -
57G ARG* 3.4 35.8 + - - +
58G ASN* 3.1 26.9 + - - -
61G PRO* 3.8 18.5 - - + +
64G ARG* 4.9 6.5 - - - +
118G LEU 5.4 3.9 + - - +
135G GLU* 3.6 35.4 - - + +
136G PHE 5.8 2.2 - - - -
137G GLN* 3.9 12.7 - - - +
138G PRO* 4.1 16.7 - - - +
423H ARG* 4.5 5.2 - - - +
427H ASP* 2.6 29.4 + - - +
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Residues in contact with ASN 125 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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446E TYR* 4.4 1.0 + - - -
123F SER 3.7 0.4 + - - -
124F ARG* 1.3 109.0 - - + +
126F VAL* 1.3 65.9 + - - +
127F GLY 3.1 10.3 + - - +
129F GLY* 3.5 18.4 + - - +
130F ILE 3.1 12.9 + - - -
131F ASP* 3.4 3.3 + - - +
58G ASN* 3.6 23.9 + - - +
59G THR 5.0 1.0 + - - -
60G PRO* 3.5 12.0 - - + +
61G PRO* 3.4 23.0 - - + +
62G LEU* 5.4 0.5 + - - +
423H ARG* 3.4 23.2 + - - +
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Residues in contact with VAL 126 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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444E VAL* 3.7 26.7 - - + +
446E TYR* 3.5 26.2 + - + +
447E HIS* 5.1 1.6 - - + -
123F SER* 3.8 20.9 - - - +
125F ASN* 1.3 76.1 - - - +
127F GLY* 1.3 58.0 + - - +
130F ILE* 2.9 34.5 + - + +
132F SER* 3.7 30.1 - - - -
478F THR* 4.6 5.2 - - + -
60G PRO* 4.7 4.0 - - - +
62G LEU* 4.3 14.9 - - - +
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Residues in contact with GLY 127 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125F ASN* 3.2 14.7 - - - +
126F VAL* 1.3 82.5 - - - +
128F PRO* 1.3 70.7 - - - +
129F GLY 3.0 9.7 + - - -
130F ILE* 3.2 21.4 + - - +
60G PRO* 4.1 8.1 - - - -
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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