Contacts of the strand formed by residues 80 - 90 (chain A) in PDB entry 3LZN
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 ILE 80 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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71A GLU* 3.6 33.7 - - + +
72A LEU 3.3 4.5 - - - +
73A LYS* 3.7 33.4 - - + +
78A GLY 3.5 12.7 + - - +
79A ALA* 1.3 80.9 - - - +
81A LYS* 1.3 65.1 + - - +
82A ARG* 3.7 27.1 + - - +
107A LYS* 5.9 1.7 + - - +
110A PHE* 3.6 6.7 - - - -
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Residues in contact with LYS 81 (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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70A TYR* 4.2 13.1 - - + +
71A GLU* 3.4 3.3 - - - +
72A LEU* 2.8 46.7 + - + +
80A ILE* 1.3 75.2 - - - +
82A ARG* 1.3 68.0 + - - +
100A ILE* 3.6 23.4 - - + +
101A ALA* 2.6 35.3 + - - +
102A MET* 5.4 0.4 - - - -
105A ASP* 2.7 28.3 + - - +
110A PHE* 3.6 27.3 - - + -
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Residues in contact with ARG 82 (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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70A TYR* 3.2 21.5 + - - +
71A GLU* 3.9 26.4 + - + -
80A ILE* 3.7 31.0 + - - +
81A LYS* 1.3 82.0 - - - +
83A GLY* 1.3 57.8 + - - +
120A TYR* 6.2 1.1 - - - -
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Residues in contact with GLY 83 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A ALA* 3.3 8.8 - - - +
70A TYR* 2.9 48.6 + - - +
82A ARG* 1.3 77.0 - - - +
84A THR* 1.3 64.5 + - - +
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Residues in contact with THR 84 (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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67A THR* 6.2 3.6 - - + -
68A ILE 3.6 12.3 - - - +
69A ALA* 4.3 9.0 - - + -
70A TYR* 3.9 1.0 - - - -
83A GLY* 1.3 79.7 - - - +
85A LEU* 1.3 67.8 - - - +
86A MET* 4.2 16.0 + - - +
97A GLY 4.5 0.2 - - - +
98A ALA* 3.5 18.0 - - - +
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Residues in contact with LEU 85 (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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43A LEU* 4.1 13.9 - - + +
44A GLU 4.9 0.4 - - - -
45A ALA* 3.7 27.6 - - + +
66A LEU 5.8 0.3 - - - +
68A ILE* 2.9 37.0 + - + +
70A TYR* 3.6 22.2 - - + -
84A THR* 1.3 76.4 - - - +
86A MET* 1.3 67.7 + - - +
87A PRO* 4.4 2.4 - - - +
96A TYR* 4.0 13.7 - - + +
97A GLY* 3.5 12.6 - - - +
98A ALA* 3.6 29.8 - - + +
119A PHE* 3.6 28.7 - - + -
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Residues in contact with MET 86 (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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27A MET* 5.1 7.9 - - + -
32A ILE* 4.0 30.1 - - + -
33A ASP* 6.0 4.3 - - + +
84A THR* 4.6 16.2 - - - +
85A LEU* 1.3 82.2 - - - +
87A PRO* 1.3 81.3 - - + +
88A MET* 3.3 14.0 + - + +
96A TYR* 3.3 3.8 - - - -
97A GLY 2.9 33.1 + - - +
128B GLY* 4.4 15.5 - - - +
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Residues in contact with PRO 87 (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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27A MET* 5.0 0.3 - - - +
62A TRP* 3.9 8.5 - - + -
66A LEU 5.6 2.0 - - - +
85A LEU 4.4 1.3 - - - +
86A MET* 1.3 101.3 - - + +
88A MET* 1.3 61.1 - - - +
95A HIS 3.4 7.2 - - - +
96A TYR* 3.9 14.3 - - + -
127A GLN* 6.0 0.7 - - - +
65B TYR* 3.6 32.8 - - + +
128B GLY 4.5 3.0 - - - +
129B PHE* 3.7 23.3 - - + +
130B GLY* 3.0 18.4 + - - -
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Residues in contact with MET 88 (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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25A ILE* 4.1 1.1 - - - -
27A MET* 3.5 27.1 - - - +
33A ASP* 5.0 3.6 - - - +
42A HIS* 3.9 7.2 - - + -
86A MET* 3.3 24.5 - - + +
87A PRO* 1.3 76.4 - - - +
89A VAL* 1.3 59.2 + - - +
94A PRO* 3.2 2.8 - - - +
95A HIS* 2.8 40.4 + - + +
97A GLY 3.3 21.5 - - - +
200A ZN 2.3 35.7 - - - -
129B PHE* 3.4 11.9 - - - -
130B GLY* 3.1 24.5 - - - +
131B ARG 4.2 0.7 - - - +
132B HIS* 3.4 10.8 - - + +
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Residues in contact with VAL 89 (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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88A MET* 1.3 75.0 - - - +
90A ALA* 1.3 70.6 + - - +
93A GLY* 3.6 19.5 - - - -
94A PRO* 3.8 1.8 - - + -
95A HIS* 5.0 0.2 - - - -
55B ASN 3.1 29.4 - - - +
56B GLY 4.0 1.1 - - - -
57B PHE* 3.7 16.6 - - + -
129B PHE* 3.6 23.3 - - + -
130B GLY 2.9 13.7 + - - +
131B ARG* 3.9 12.5 - - + +
132B HIS* 3.0 28.2 + - - -
139B VAL* 4.2 4.1 - - + +
142B TRP* 4.0 10.3 - - + -
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Residues in contact with ALA 90 (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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44A GLU* 5.2 0.7 - - - +
89A VAL* 1.3 79.8 - - - +
91A ASP* 1.3 64.7 + - - +
92A ASP* 3.0 18.8 - - - +
93A GLY 2.9 23.5 + - - +
95A HIS* 4.2 4.7 + - + -
56B GLY* 3.5 2.4 - - - -
132B HIS* 3.4 34.3 - - + +
137B THR* 3.5 10.1 - - - +
139B VAL* 3.3 14.2 - - - +
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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