Contacts of the strand formed by residues 93 - 100 (chain A) in PDB entry 3LZP
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 93 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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89A VAL* 3.6 7.0 - - - -
90A ALA* 3.0 23.8 + - - +
92A ASP* 1.3 81.8 - - - +
94A PRO* 1.3 77.9 - - - +
95A HIS* 3.7 7.4 + - - -
56B GLY 3.2 17.0 + - - -
58B PRO* 3.9 4.7 - - - -
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Residues in contact with PRO 94 (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 ASP* 5.1 0.5 - - - +
48A HIS* 4.6 8.5 + - - -
62A TRP* 3.5 56.8 - - + -
88A MET 3.2 11.9 - - - +
89A VAL* 3.8 3.1 - - + -
93A GLY* 1.3 87.5 - - - +
95A HIS* 1.3 63.2 + - - +
57B PHE* 3.7 32.1 - - + -
58B PRO* 3.9 16.6 - - + -
61B PHE* 4.1 8.3 - - + -
129B PHE* 4.4 0.9 - - + -
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Residues in contact with HIS 95 (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* 3.0 34.4 + - + +
45A ALA 3.9 3.8 - - - +
46A ASP* 3.8 22.2 - - - +
62A TRP* 3.7 11.9 - - - +
87A PRO* 3.5 4.0 - - - +
88A MET* 2.9 40.7 + - + +
90A ALA* 3.8 15.1 - - + +
92A ASP* 5.1 2.8 + - - -
93A GLY 3.7 10.1 + - - -
94A PRO* 1.3 75.7 - - - +
96A TYR* 1.3 77.9 + - - +
97A GLY 3.9 0.2 - - - -
200A CU 2.0 31.8 - - - -
132B HIS* 3.2 15.3 - + - -
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Residues in contact with TYR 96 (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* 3.1 6.4 - - - +
45A ALA* 2.9 39.0 + - + +
47A ILE* 4.5 5.8 - - + -
62A TRP* 3.4 26.2 - + - -
63A MET 2.6 29.1 + - - -
64A PRO* 3.2 1.2 - - - +
65A TYR 3.2 8.0 + - - -
66A LEU* 3.0 48.4 + - + +
68A ILE* 3.5 29.2 - - + -
85A LEU* 3.9 23.9 - - + +
86A MET 3.3 5.8 - - - -
87A PRO* 3.9 28.5 - - + -
95A HIS* 1.3 74.7 - - - +
97A GLY* 1.3 58.9 + - - +
65B TYR* 4.2 2.2 - - - -
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Residues in contact with GLY 97 (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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42A HIS* 4.0 7.6 - - - -
43A LEU 3.0 11.9 - - - -
85A LEU* 3.7 5.8 - - - +
86A MET* 2.9 34.0 + - - +
88A MET* 3.4 23.3 - - - +
95A HIS* 4.1 2.2 - - - -
96A TYR* 1.3 75.4 - - - +
98A ALA* 1.3 62.7 + - - +
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Residues in contact with ALA 98 (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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33A ASP* 3.4 15.5 - - - +
42A HIS* 3.4 8.4 - - - -
43A LEU* 2.8 34.4 + - - -
70A TYR* 4.4 11.2 - - + +
84A THR 4.3 10.5 - - - +
85A LEU* 3.5 17.3 - - + -
97A GLY* 1.3 75.9 - - - +
99A ASN* 1.3 67.8 + - - +
100A ILE* 3.7 7.5 + - + +
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Residues in contact with ASN 99 (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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24A PRO* 3.5 5.4 - - - +
25A ILE 2.7 39.8 + - - +
27A MET* 6.0 1.2 - - - +
33A ASP* 2.8 19.6 + - - +
34A LEU* 2.8 46.1 + - + +
36A ALA* 3.6 13.3 - - - +
39A ALA* 3.8 13.5 - - + -
41A ILE 3.4 2.5 - - - -
42A HIS* 2.9 21.3 + - - +
70A TYR* 5.3 0.5 + - - -
98A ALA* 1.3 75.1 - - - +
100A ILE* 1.3 63.6 + - - +
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Residues in contact with ILE 100 (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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34A LEU* 4.2 0.7 - - - -
39A ALA* 3.9 2.2 - - - +
40A ASP* 2.9 20.3 + - - -
41A ILE* 2.8 27.8 + - + +
43A LEU* 3.6 40.2 - - + -
70A TYR* 3.8 30.1 - - + +
72A LEU* 4.4 7.9 - - + -
81A LYS* 3.7 21.3 - - + +
98A ALA* 3.8 8.7 - - + +
99A ASN* 1.3 80.7 - - - +
101A ALA* 1.3 75.5 + - - +
102A MET* 3.7 15.4 + - - -
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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