Contacts of the helix formed by residues 70 - 78 (chain A) in PDB entry 2ZLB
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 70 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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29A ILE* 4.4 1.6 - - - -
69A CYS* 1.3 76.0 - - - +
71A TYR* 1.3 64.5 + - - +
72A SER 3.3 2.5 - - - -
73A ALA* 3.3 4.4 + - - +
74A VAL* 3.0 31.2 + - - +
99A THR* 3.3 34.1 + - - -
102A MET* 4.6 3.6 - - - -
300A SO4 3.1 8.3 + - - -
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Residues in contact with TYR 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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26A LEU* 3.4 41.9 - - + +
29A ILE* 3.6 40.9 - - + +
30A ASP* 4.3 12.9 + - + -
38A TRP* 4.1 14.1 - + + -
43A GLY* 3.5 32.4 + - - -
44A ASP 4.0 0.9 + - - -
46A LYS* 4.6 11.4 - - + -
47A GLY* 4.6 2.9 - - - -
50A MET* 5.5 0.4 - - - -
69A CYS* 3.3 6.0 + - - -
70A GLY* 1.3 75.8 - - - +
72A SER* 1.3 59.9 + - - +
74A VAL 3.2 0.2 + - - -
75A ARG* 2.8 78.0 + - + +
300A SO4 3.5 15.3 + - - +
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Residues in contact with SER 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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46A LYS* 3.4 26.0 + - - -
50A MET* 3.9 9.6 - - - -
64A GLU* 4.0 11.7 - - - -
70A GLY 3.3 0.4 - - - -
71A TYR* 1.3 74.3 - - - +
73A ALA* 1.3 57.3 + - - +
75A ARG* 3.3 3.4 + - - +
76A MET* 3.0 36.0 + - - +
139A PHE* 3.6 25.1 - - - -
141A ASP* 3.7 1.7 + - - -
300A SO4 2.6 26.4 + - - -
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Residues in contact with ALA 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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64A GLU* 3.4 22.4 + - - +
70A GLY* 3.3 9.2 + - - +
72A SER* 1.3 75.0 - - - +
74A VAL* 1.3 60.5 + - - +
76A MET* 4.5 0.2 - - - -
77A ALA* 2.9 34.3 + - - +
86A LEU* 3.7 16.8 - - + +
88A THR* 4.4 1.6 - - + -
99A THR* 4.0 14.4 - - + -
103A LEU* 3.8 23.1 - - + -
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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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22A PRO* 4.0 24.5 - - + +
25A VAL* 4.3 7.9 - - + -
26A LEU* 3.6 24.7 - - + -
29A ILE* 5.1 0.2 - - + -
70A GLY 3.0 20.5 + - - +
71A TYR* 3.7 4.3 - - - +
73A ALA* 1.3 74.8 - - - +
75A ARG* 1.3 57.4 + - - +
78A ARG* 2.9 36.2 + - - +
102A MET* 3.9 33.4 - - + +
103A LEU* 3.8 21.1 - - + +
106A ALA* 4.2 6.1 - - + -
108A LEU* 3.7 5.2 - - + +
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Residues in contact with ARG 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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23A GLN* 6.1 0.4 - - - -
26A LEU* 3.6 18.2 - - + +
43A GLY 4.6 1.6 + - - -
44A ASP* 5.1 4.2 - - - +
47A GLY* 3.3 28.0 - - - -
48A GLN* 2.7 24.2 + - - +
50A MET* 3.8 20.0 - - + -
51A ASP* 2.7 41.6 + - - +
71A TYR* 2.8 51.4 + - + +
72A SER* 3.4 7.6 - - - +
74A VAL* 1.3 78.8 - - - +
76A MET* 1.3 62.6 + - - +
78A ARG* 2.8 40.0 + - - +
79A LEU* 3.8 5.0 - - - +
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Residues in contact with MET 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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50A MET* 3.6 14.1 - - + -
54A ILE* 3.7 29.6 - - + +
62A VAL* 4.0 15.5 - - + -
64A GLU* 3.6 31.2 - - + +
72A SER 3.0 15.1 + - - +
73A ALA* 4.1 2.0 - - - +
75A ARG* 1.3 76.2 - - - +
77A ALA* 1.3 60.1 + - - +
79A LEU* 2.9 23.8 + - - +
80A LEU* 3.4 18.5 + - + +
86A LEU* 4.0 15.3 - - + -
137A MET* 4.3 4.0 - - - -
139A PHE* 3.7 43.5 - - + -
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Residues in contact with ALA 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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73A ALA 2.9 23.0 + - - +
76A MET* 1.3 73.1 - - - +
78A ARG* 1.3 62.9 + - - +
79A LEU 2.9 1.6 + - - -
80A LEU* 3.1 28.6 + - + +
86A LEU* 4.3 2.9 - - + +
103A LEU* 4.1 0.9 - - + -
108A LEU* 3.9 25.1 - - + +
111A LYS* 4.3 10.6 - - + +
112A VAL* 3.7 28.5 - - + -
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Residues in contact with ARG 78 (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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22A PRO* 3.7 27.4 - - + -
23A GLN* 4.3 17.3 + - - +
26A LEU* 3.6 25.3 - - - +
51A ASP* 2.8 39.6 + - - -
55A ARG* 4.5 6.1 - - - +
74A VAL 2.9 13.1 + - - +
75A ARG* 2.8 48.8 + - - +
76A MET 3.2 0.4 - - - -
77A ALA* 1.3 77.2 - - - +
79A LEU* 1.3 79.3 + - + +
80A LEU 3.9 2.3 + - - +
108A LEU* 3.7 12.5 - - + +
111A LYS* 5.8 1.6 - - - -
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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