Contacts of the strand formed by residues 120 - 127 (chain H) 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 H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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120E GLY 3.8 0.2 - - - +
121E GLU* 3.4 8.3 - - - +
122E HIS* 2.8 30.9 + - - -
118H LEU 3.2 5.3 + - - -
119H LYS* 1.3 76.9 - - - +
121H GLU* 1.3 64.6 + - - +
134H SER* 3.3 22.7 - - - -
135H GLU* 5.0 1.3 - - - +
136H PHE* 4.0 12.1 - - - -
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Residues in contact with GLU 121 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116E GLU* 4.4 6.2 - - - +
119E LYS* 2.8 50.9 + - + +
120E GLY 3.4 6.7 - - - +
122E HIS* 4.5 0.9 - - - -
446G TYR 4.6 0.2 - - - +
447G HIS* 3.6 13.0 + - + -
465G PRO* 4.0 13.7 - - - +
119H LYS 5.4 1.6 - - - +
120H GLY* 1.3 76.1 - - - +
122H HIS* 1.3 59.0 + - - +
133H TRP* 3.3 3.5 - - - -
134H SER* 2.7 39.1 + - - +
136H PHE* 5.7 6.1 - - + -
474H ARG* 5.1 5.3 + - - -
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Residues in contact with HIS 122 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118E LEU 4.3 0.9 - - - +
119E LYS* 3.3 5.8 - - - -
120E GLY 2.7 46.6 + - - +
122E HIS* 3.8 16.7 + - + +
133E TRP* 3.5 43.9 + + + -
134E SER 4.3 4.9 - - - +
135E GLU* 3.3 30.3 + - + -
120H GLY 4.1 1.2 + - - -
121H GLU* 1.3 71.3 - - - +
123H SER* 1.3 73.5 + - - +
124H ARG* 4.3 2.3 + - + -
131H ASP* 4.1 14.2 + - + -
132H SER 4.8 0.7 - - - -
133H TRP* 3.8 35.0 - + - +
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Residues in contact with SER 123 (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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115E PRO 5.0 0.8 + - - -
118E LEU 5.5 0.4 - - - -
119E LYS* 3.9 13.7 - - - +
446G TYR* 3.7 13.1 - - - -
447G HIS* 2.8 29.3 + - - -
121H GLU 4.1 0.2 + - - -
122H HIS* 1.3 77.7 + - - +
124H ARG* 1.3 62.9 + - - +
126H VAL* 3.7 19.2 - - - +
131H ASP* 3.6 3.6 - - - +
132H SER 2.7 43.5 + - - +
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Residues in contact with ARG 124 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57E ARG* 3.4 33.4 + - - +
58E ASN* 3.0 27.3 + - - -
61E PRO* 3.6 19.5 - - - +
64E ARG* 4.9 6.7 - - - +
118E LEU 5.5 2.8 + - - -
135E GLU* 3.5 37.0 - - + +
136E PHE 6.4 0.4 - - - -
137E GLN* 3.8 11.9 - - - +
138E PRO* 4.1 17.4 - - - +
423F ARG* 4.4 3.4 - - - +
427F ASP* 2.7 27.6 + - - -
446G TYR* 5.2 1.0 + - - -
122H HIS* 4.3 2.9 + - + -
123H SER* 1.3 71.7 - - - +
125H ASN* 1.3 89.0 + - - +
126H VAL* 4.6 0.7 - - - +
131H ASP* 3.8 13.9 - - - +
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Residues in contact with ASN 125 (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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58E ASN* 3.4 30.5 + - - +
59E THR 5.0 0.6 + - - -
60E PRO* 3.4 13.6 - - + +
61E PRO* 3.4 23.2 - - + +
423F ARG* 3.8 14.2 + - - +
446G TYR* 4.4 1.2 + - - -
124H ARG* 1.3 107.0 - - + +
126H VAL* 1.3 63.7 + - - +
127H GLY 3.1 8.2 + - - +
128H PRO* 4.9 0.7 - - - -
129H GLY* 3.3 27.1 + - - -
130H ILE 3.1 15.8 + - - -
131H ASP* 3.3 4.0 + - - -
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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
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60E PRO* 4.8 3.1 - - - +
62E LEU* 4.2 17.9 - - - +
444G VAL* 3.6 23.4 - - + +
446G TYR* 3.4 27.4 - - + +
447G HIS* 5.4 1.1 - - + -
123H SER* 3.7 30.3 - - - +
124H ARG 4.9 0.4 - - - -
125H ASN* 1.3 73.2 - - - +
127H GLY* 1.3 58.5 + - - +
130H ILE* 3.0 29.1 + - + +
132H SER* 3.9 22.7 - - - -
478H THR* 4.6 5.4 - - + -
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Residues in contact with GLY 127 (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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60E PRO* 4.1 8.3 - - - -
125H ASN* 3.4 9.7 - - - -
126H VAL* 1.3 80.7 - - - +
128H PRO* 1.3 78.4 - - - +
129H GLY 3.2 0.5 + - - -
130H ILE* 3.0 27.3 + - - +
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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