Contacts of the strand formed by residues 120 - 127 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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118A LEU 3.3 4.6 + - - -
119A LYS* 1.3 76.6 - - - +
121A GLU* 1.3 60.1 + - - +
134A SER* 3.5 22.9 - - - -
135A GLU* 5.0 0.9 - - - -
136A PHE* 3.9 12.3 - - - -
121D GLU* 3.5 7.1 - - - +
122D HIS* 2.7 35.8 + - - -
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Residues in contact with GLU 121 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119A LYS 5.7 0.4 - - - +
120A GLY* 1.3 75.8 - - - -
122A HIS* 1.3 59.5 + - - +
133A TRP* 3.2 4.8 - - - -
134A SER* 2.8 43.8 + - - +
136A PHE* 5.7 3.4 - - + -
474A ARG* 4.4 9.7 + - - -
447B HIS* 3.6 12.0 - - + -
465B PRO* 3.9 15.4 - - - +
116D GLU* 4.4 5.9 - - - +
119D LYS* 3.3 48.8 + - + +
120D GLY 3.4 6.3 - - - +
122D HIS* 4.4 0.4 - - - -
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Residues in contact with HIS 122 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120A GLY 4.2 0.4 + - - -
121A GLU* 1.3 73.7 - - - +
123A SER* 1.3 76.5 + - - +
124A ARG 4.3 1.7 + - - -
131A ASP* 4.5 13.3 + - + +
133A TRP* 3.7 27.7 - + - +
118D LEU 4.2 0.7 - - - +
119D LYS* 3.5 5.4 - - - -
120D GLY* 2.7 48.4 + - - +
122D HIS* 3.6 25.6 + - + -
133D TRP* 3.3 48.1 + + + -
134D SER 4.4 2.9 - - - +
135D GLU* 3.6 20.0 + - + -
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Residues in contact with SER 123 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122A HIS* 1.3 78.6 + - - +
124A ARG* 1.3 62.6 + - - +
126A VAL* 3.9 19.0 - - - +
131A ASP* 3.5 5.2 - - - +
132A SER 2.7 38.2 + - - +
446B TYR* 3.5 18.1 - - - -
447B HIS* 3.0 25.9 + - - -
115D PRO 4.5 1.0 + - - -
118D LEU 5.3 1.8 - - - -
119D LYS* 4.0 12.0 - - - +
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Residues in contact with ARG 124 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122A HIS* 4.2 3.3 + - + -
123A SER* 1.3 72.5 - - - +
125A ASN* 1.3 88.7 + - - +
126A VAL* 3.6 0.7 + - - -
131A ASP* 3.6 11.4 - - - +
446B TYR* 5.2 1.0 + - - -
423C ARG* 4.8 0.7 - - - +
427C ASP* 2.7 31.7 + - - +
57D ARG* 3.3 36.8 + - - +
58D ASN* 3.1 27.1 + - - -
59D THR 5.6 0.6 + - - -
61D PRO* 3.7 20.2 - - + +
64D ARG* 4.9 6.5 - - - +
118D LEU 5.3 4.5 + - - +
135D GLU* 3.5 33.9 - - + +
136D PHE 6.0 0.7 - - - -
137D GLN* 4.0 13.9 - - - +
138D PRO* 4.4 12.5 - - - +
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Residues in contact with ASN 125 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123A SER 3.8 0.4 + - - -
124A ARG* 1.3 108.2 - - + +
126A VAL* 1.3 66.3 + - - +
127A GLY 3.0 10.3 + - - +
128A PRO* 4.9 0.2 - - - -
129A GLY* 3.2 28.1 + - - +
130A ILE 3.1 7.2 + - - -
131A ASP* 3.0 13.3 + - - -
446B TYR* 4.5 0.5 + - - -
423C ARG* 3.7 15.6 + - - +
427C ASP* 5.3 0.2 + - - -
58D ASN* 3.5 25.4 + - - +
59D THR 5.1 0.4 + - - -
60D PRO* 3.4 20.6 - - + +
61D PRO* 3.6 14.1 - - + +
62D LEU 5.5 0.2 + - - -
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Residues in contact with VAL 126 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123A SER* 3.9 24.7 - - - +
125A ASN* 1.3 72.7 - - - +
127A GLY* 1.3 59.4 + - - +
130A ILE* 2.8 32.4 + - + +
132A SER* 3.9 24.9 - - - +
478A THR* 4.7 4.0 - - + -
444B VAL* 3.7 28.8 - - + +
446B TYR* 3.5 22.4 - - + +
447B HIS* 5.2 1.6 - - + -
60D PRO* 4.8 3.3 - - - +
62D LEU* 4.1 17.8 - - - +
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Residues in contact with GLY 127 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125A ASN* 3.3 14.3 - - - -
126A VAL* 1.3 83.1 - - - +
128A PRO* 1.3 77.1 - - - +
129A GLY 3.0 1.4 + - - -
130A ILE* 3.0 23.0 + - - +
60D PRO* 4.0 7.9 - - - -
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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