Contacts of the strand formed by residues 120 - 127 (chain I) 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 I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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118I LEU 3.3 4.4 + - - -
119I LYS* 1.3 76.8 - - - +
121I GLU* 1.3 64.9 + - - +
134I SER* 3.3 23.8 - - - -
135I GLU* 5.0 2.0 - - - -
136I PHE* 4.3 9.2 - - - -
121J GLU* 3.5 8.1 - - - +
122J HIS* 2.8 31.8 + - - -
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Residues in contact with GLU 121 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119I LYS 5.4 1.1 - - - +
120I GLY* 1.3 77.9 - - - +
122I HIS* 1.3 60.9 + - - +
123I SER 4.1 0.2 - - - -
133I TRP* 3.2 5.1 - - - +
134I SER* 2.9 39.3 + - - +
136I PHE* 5.8 6.2 - - + -
474I ARG* 5.0 6.9 + - - -
116J GLU* 4.3 6.8 - - - +
119J LYS* 3.0 50.4 + - + +
120J GLY 3.4 5.4 - - - +
122J HIS* 4.5 0.4 - - - -
447L HIS* 3.9 10.4 + - + -
465L PRO* 4.0 12.3 - - - +
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Residues in contact with HIS 122 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120I GLY 4.1 0.6 + - - -
121I GLU* 1.3 73.3 - - - +
123I SER* 1.3 76.1 + - - +
124I ARG 4.1 2.9 + - - -
131I ASP* 4.4 11.9 + - + -
132I SER 4.8 1.1 - - - -
133I TRP* 3.6 36.4 - + + +
118J LEU 4.3 0.9 - - - +
119J LYS* 3.4 5.3 - - - -
120J GLY 2.8 45.0 + - - +
122J HIS* 3.8 14.7 + - + +
133J TRP* 3.3 49.5 + + + -
134J SER 4.2 5.2 - - - +
135J GLU* 3.5 20.9 + - + -
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Residues in contact with SER 123 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121I GLU 4.1 0.2 + - - -
122I HIS* 1.3 76.4 + - - +
124I ARG* 1.3 63.9 + - - +
126I VAL* 3.8 19.7 - - - +
131I ASP* 3.6 5.2 - - - +
132I SER 2.6 40.0 + - - +
115J PRO 5.5 1.3 - - - -
118J LEU 5.6 0.9 - - - -
119J LYS* 4.0 12.0 - - - +
446L TYR* 3.7 12.9 - - - -
447L HIS* 2.7 29.4 + - - -
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Residues in contact with ARG 124 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122I HIS* 4.1 5.3 + - + -
123I SER* 1.3 72.8 - - - +
125I ASN* 1.3 92.1 + - - +
126I VAL* 3.6 0.9 + - - -
131I ASP* 3.6 10.1 - - - +
57J ARG* 3.3 33.4 + - - +
58J ASN* 3.0 27.1 + - - -
61J PRO* 3.7 16.7 - - + +
64J ARG* 4.8 5.7 - - - +
118J LEU 5.5 4.1 + - - +
135J GLU* 3.6 31.0 - - + +
136J PHE 6.0 1.1 - - - -
137J GLN* 3.9 10.5 - - - +
138J PRO* 3.8 20.0 - - - +
423K ARG* 4.9 1.3 - - - +
427K ASP* 2.6 33.5 + - - +
446L TYR* 5.1 1.4 + - - -
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Residues in contact with ASN 125 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123I SER 3.7 0.2 + - - -
124I ARG* 1.3 110.5 - - + +
126I VAL* 1.3 64.1 + - - +
127I GLY 3.1 9.4 - - - +
128I PRO* 5.0 0.2 - - - -
129I GLY* 3.3 27.5 + - - -
130I ILE 3.0 7.7 + - - -
131I ASP* 3.0 13.1 + - - -
57J ARG 4.8 0.2 + - - -
58J ASN* 3.9 22.1 + - - +
59J THR 5.3 0.8 + - - -
60J PRO* 3.5 13.4 - - + +
61J PRO* 3.3 23.1 - - + +
62J LEU 5.4 0.2 + - - -
423K ARG* 3.6 16.8 + - - +
446L TYR* 4.5 0.9 + - - -
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Residues in contact with VAL 126 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123I SER* 3.8 19.1 - - - +
125I ASN* 1.3 75.4 - - - +
127I GLY* 1.3 58.4 + - - +
130I ILE* 2.7 33.9 + - + +
132I SER* 3.8 29.8 - - - -
478I THR* 4.5 4.9 - - + -
60J PRO* 4.6 4.5 - - - +
62J LEU* 4.4 14.6 - - - +
444L VAL* 3.7 27.4 - - + +
446L TYR* 3.4 26.2 + - + +
447L HIS* 5.2 1.1 - - + -
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Residues in contact with GLY 127 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125I ASN* 3.3 11.7 - - - -
126I VAL* 1.3 83.1 - - - +
128I PRO* 1.3 76.7 - - - +
129I GLY 3.0 4.3 + - - -
130I ILE* 3.0 21.1 + - - +
60J PRO* 4.0 10.8 - - - -
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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