Contacts of the strand formed by residues 15 - 22 (chain B) 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 MET 15 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10B LYS 3.7 0.3 - - - +
11B GLU* 3.3 4.2 - - - -
12B LEU 2.9 31.8 + - - +
13B ASN* 3.7 11.7 - - + +
14B GLY* 1.3 83.9 - - - +
16B GLU* 1.3 59.6 + - - +
17B ILE* 4.0 6.8 + - + +
47B ILE* 3.7 27.6 - - + -
48B HIS 3.3 8.5 - - - +
50B LEU* 3.5 8.0 - - - +
53B ASN* 4.5 0.4 - - - +
63B MET* 3.8 35.0 - - + -
66B LEU* 4.3 7.6 - - - -
121B ILE* 4.9 2.5 - - + -
143B PHE* 3.4 35.7 - - + -
146B PHE* 3.8 25.4 - - + -
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Residues in contact with GLU 16 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9B PRO* 4.2 24.0 - - + +
10B LYS 3.4 8.3 - - - +
11B GLU* 4.9 8.4 - - + +
15B MET* 1.3 71.4 - - - +
17B ILE* 1.3 62.9 + - - +
18B ALA* 4.8 6.8 - - + +
46B ASP 3.3 3.0 - - - +
47B ILE* 3.2 6.8 - - - +
48B HIS* 2.8 41.8 + - + +
49B ALA 5.8 0.2 - - - +
50B LEU* 3.5 19.7 - - + +
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Residues in contact with ILE 17 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B PRO* 3.5 1.8 - - - +
10B LYS* 2.8 33.4 + - + +
12B LEU* 4.0 27.4 - - + +
15B MET* 4.2 6.3 - - + +
16B GLU* 1.3 77.6 - - - +
18B ALA* 1.3 61.1 + - - +
46B ASP 3.5 2.0 - - - -
47B ILE* 4.1 25.8 - - + -
119B PHE* 4.6 6.1 - - + -
121B ILE* 4.1 19.3 - - + -
146B PHE* 3.8 34.5 - - + -
148B VAL* 4.3 10.5 - - + -
150B TYR* 3.0 26.5 + - - +
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Residues in contact with ALA 18 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9B PRO* 3.8 22.9 - - + -
16B GLU* 4.1 8.3 - - + +
17B ILE* 1.3 75.2 - - - +
19B ALA* 1.3 64.0 + - - +
20B VAL* 5.3 3.8 - - + -
45B ALA* 3.3 6.6 - - - +
46B ASP* 2.8 49.3 + - + +
119B PHE* 4.4 0.5 - - - -
150B TYR* 4.1 2.2 - - - -
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Residues in contact with ALA 19 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5B PRO* 3.9 1.0 - - - +
6B ILE* 2.9 42.8 + - + +
8B ASP 6.1 0.2 - - - -
18B ALA* 1.3 74.9 - - - +
20B VAL* 1.3 68.1 + - - +
44B GLU 3.4 5.6 - - - +
117B LEU* 4.0 11.7 - - + -
119B PHE* 3.8 22.4 - - + -
150B TYR* 3.9 18.0 + - + -
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Residues in contact with VAL 20 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3B GLU* 4.0 31.4 - - + +
4B VAL 3.2 15.5 - - - +
5B PRO* 4.0 11.0 - - + -
6B ILE* 3.6 6.5 - - - -
18B ALA* 5.3 4.7 - - + -
19B ALA* 1.3 81.0 - - - +
21B TYR* 1.3 62.3 + - - +
22B LEU* 4.2 2.5 - - + -
43B LEU* 3.7 4.7 - - - +
44B GLU* 2.9 59.6 + - + +
46B ASP* 4.0 12.1 - - - +
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Residues in contact with TYR 21 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2B GLY 3.9 0.7 - - - +
3B GLU* 3.6 2.8 - - - -
4B VAL* 2.8 70.3 + - + +
6B ILE* 3.8 21.3 - - + -
20B VAL* 1.3 74.9 - - - +
22B LEU* 1.3 63.3 + - - +
41B ILE* 3.6 33.2 - - + -
42B HIS 3.1 10.3 - - - +
43B LEU* 4.5 1.3 - - + -
152B PHE* 3.7 26.0 - + - -
153B LYS 3.9 3.5 + - - -
154B TYR* 3.8 12.9 - + - -
155B THR* 3.6 31.0 + - - -
156B GLY 3.8 16.9 + - - -
158B PRO* 3.8 15.5 - - + -
159B LYS* 5.3 0.3 + - - -
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Residues in contact with LEU 22 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132A HIS* 5.1 5.6 - - + -
137A THR* 6.0 3.8 - - + -
2B GLY 3.5 10.3 - - - +
3B GLU* 3.7 25.8 - - + +
20B VAL* 4.2 2.2 - - + -
21B TYR* 1.3 77.2 - - - +
23B GLN* 1.3 76.1 + - - +
25B ILE* 4.3 20.6 - - + -
41B ILE* 3.3 9.7 - - - +
42B HIS* 2.8 61.7 + - + +
44B GLU* 3.5 34.1 - - + +
158B PRO* 3.7 9.2 - - - +
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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
------------------------------------------------------------
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