Contacts of the strand formed by residues 69 - 77 (chain A) in PDB entry 4ZCH
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 THR 69 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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67A THR 3.7 4.2 + - - +
68A PHE* 1.3 70.5 - - - +
70A MET* 1.3 62.0 + - - +
89A ILE* 4.9 2.2 - - - -
90A ARG 3.4 8.7 - - - -
91A SER* 3.3 29.8 - - - +
123A ARG* 3.2 25.6 + - - +
248A LEU* 4.3 14.8 - - + +
250A ASN* 4.3 20.8 + - + -
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Residues in contact with MET 70 (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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63A PHE* 3.6 29.8 - - + -
65A ASP* 3.3 37.9 - - + +
68A PHE* 3.8 4.9 - - - +
69A THR* 1.3 76.2 - - - +
71A GLY* 1.3 58.9 + - - +
89A ILE* 3.4 10.2 - - - +
90A ARG* 2.9 30.8 + - + +
92A MET* 3.5 27.4 - - + -
121A ILE* 3.7 25.1 - - + -
123A ARG* 3.7 35.9 - - + -
126A ALA* 4.2 3.6 - - + -
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Residues in contact with GLY 71 (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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63A PHE* 3.7 18.3 - - - -
70A MET* 1.3 77.7 - - - +
72A GLN* 1.3 60.6 + - - -
73A VAL* 5.4 0.7 - - - -
88A CYS 2.7 21.3 - - - -
89A ILE* 4.3 5.8 - - - -
90A ARG 4.7 0.4 - - - -
121A ILE* 4.1 5.7 - - - +
122A PRO* 3.4 23.6 - - - +
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Residues in contact with GLN 72 (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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59A SER* 3.3 36.4 + - - +
61A VAL* 3.6 19.7 - - + +
63A PHE* 3.6 8.1 - - - -
71A GLY* 1.3 72.6 - - - -
73A VAL* 1.3 62.2 + - - +
74A VAL* 4.0 6.3 + - + +
86A PHE* 4.1 2.4 - - + +
87A ARG* 3.3 6.8 - - - +
88A CYS* 3.2 39.5 + - - +
103A CYS* 3.1 39.5 + - - +
105A SER* 4.7 1.6 - - - +
119A VAL* 3.7 20.0 - - + -
120A ILE 3.4 6.1 - - - +
121A ILE* 4.2 6.7 - - + -
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Residues in contact with VAL 73 (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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71A GLY 5.0 0.9 - - - +
72A GLN* 1.3 76.5 - - - +
74A VAL* 1.3 65.3 + - - +
75A SER* 3.8 8.3 + - - +
84A THR* 3.8 31.6 - - + +
86A PHE 3.9 2.7 - - - -
87A ARG* 3.8 20.0 - - + -
89A ILE* 6.4 0.7 - - + -
118A SER 3.6 0.9 - - - +
119A VAL* 3.4 3.2 - - - -
120A ILE* 2.7 51.4 + - + +
122A PRO* 3.8 27.8 - - + -
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Residues in contact with VAL 74 (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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57A LEU* 3.9 31.4 - - + -
59A SER* 3.6 33.9 - - - +
72A GLN* 4.0 4.2 + - + -
73A VAL* 1.3 71.0 - - - +
75A SER* 1.3 63.0 + - - +
84A THR* 3.7 2.6 - - - +
85A LEU* 2.9 30.4 + - + -
86A PHE* 2.9 36.0 + - + +
117A LEU* 5.1 3.4 - - + -
118A SER 3.3 7.0 - - - +
119A VAL* 3.8 16.8 - - + -
137A LEU* 5.0 1.6 - - + -
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Residues in contact with SER 75 (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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73A VAL* 3.8 9.2 + - - +
74A VAL* 1.3 75.5 - - - +
76A ARG* 1.3 62.4 + - - +
82A GLN* 4.7 15.7 + - - +
83A GLU 3.3 20.6 - - - -
84A THR* 4.1 7.2 - - - -
85A LEU* 4.3 4.3 - - - +
116A ILE 3.6 0.7 - - - +
117A LEU* 3.2 6.1 - - - +
118A SER* 2.8 51.7 + - - -
120A ILE* 4.9 7.6 - - - +
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Residues in contact with ARG 76 (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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75A SER* 1.3 72.8 - - - +
77A GLU* 1.3 58.8 - - - +
81A ARG* 3.4 26.9 - - - +
82A GLN* 3.5 2.0 - - - -
83A GLU* 2.8 67.6 + - + +
85A LEU* 3.7 23.7 - - + +
109A PHE* 5.3 3.6 - - - +
110A HIS* 2.9 25.6 + - - +
111A LEU* 3.9 7.8 - - - +
112A HIS* 3.0 28.6 + - - -
115A ASP* 2.8 36.8 + - - +
116A ILE 3.2 4.0 - - - -
117A LEU* 3.9 22.9 - - + -
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Residues in contact with GLU 77 (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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76A ARG* 1.3 69.2 - - - +
78A GLY* 1.3 62.7 + - - +
80A GLY 6.4 1.1 - - - -
81A ARG 4.1 5.2 - - - +
82A GLN* 3.6 29.3 + - - +
114A GLY 4.3 2.6 - - - +
115A ASP* 3.5 2.3 - - - -
116A ILE* 2.7 68.8 + - + +
118A SER* 5.7 1.8 + - - +
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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