Contacts of the strand formed by residues 41 - 49 (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 ILE 41 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21B TYR* 3.6 35.2 - - + -
22B LEU 3.3 9.4 - - - +
24B PRO* 3.6 7.6 - - - +
39B ALA* 4.0 1.6 - - - +
40B ASP* 1.3 84.4 - - - +
42B HIS* 1.3 62.8 + - - +
43B LEU* 4.5 11.2 - - + +
72B LEU* 5.0 4.5 - - + -
99B ASN* 3.3 6.1 - - - +
100B ILE* 2.8 48.1 + - + +
102B MET* 4.0 24.2 - - + -
152B PHE* 5.7 4.5 - - + -
154B TYR* 3.5 32.3 - - + +
158B PRO* 4.4 3.6 - - + -
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Residues in contact with HIS 42 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B TYR* 3.1 5.7 - - - -
22B LEU* 2.8 59.6 + - + +
23B GLN 3.3 19.7 + - - +
25B ILE* 3.6 14.6 - - + +
27B MET* 5.8 0.9 - - + -
33B ASP* 4.8 1.3 - - - -
41B ILE* 1.3 74.4 - - - +
43B LEU* 1.3 64.6 + - - +
44B GLU* 4.2 1.3 - - + -
88B MET* 3.8 9.9 - - + -
95B HIS* 3.2 10.0 + - - -
97B GLY* 3.5 7.7 - - - -
98B ALA* 3.4 23.6 - - - -
99B ASN* 2.9 24.5 + - - +
200B ZN 2.5 33.4 - - - -
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Residues in contact with LEU 43 (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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6B ILE* 3.6 31.0 - - + -
19B ALA* 5.2 0.2 - - + -
20B VAL 3.7 1.8 - - - +
21B TYR* 4.5 3.8 - - + -
41B ILE* 4.1 8.0 - - + +
42B HIS* 1.3 72.6 - - - +
44B GLU* 1.3 65.8 + - - +
70B TYR* 4.1 17.3 - - + -
72B LEU* 5.1 5.6 - - + -
85B LEU* 3.9 10.5 - - + +
97B GLY* 3.1 5.2 - - - -
98B ALA 2.9 31.9 + - - +
100B ILE* 3.7 32.8 - - + -
117B LEU* 3.8 35.0 - - + -
119B PHE* 4.3 8.3 - - + -
152B PHE* 5.9 1.6 - - + -
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Residues in contact with GLU 44 (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* 4.8 5.8 - - - +
19B ALA* 3.4 6.6 - - - +
20B VAL* 2.9 51.8 + - + +
22B LEU* 3.5 29.5 - - + +
42B HIS* 4.2 0.9 - - + -
43B LEU* 1.3 76.3 - - - +
45B ALA* 1.3 59.3 + - - +
46B ASP* 2.4 34.1 - - - +
85B LEU* 4.5 2.9 - - - -
95B HIS* 3.4 38.4 + - + +
96B TYR 3.2 5.2 - - - +
119B PHE* 4.2 3.5 - - - -
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Residues in contact with ALA 45 (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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17B ILE* 5.6 0.2 - - + -
18B ALA 3.3 6.3 - - - +
44B GLU* 1.3 71.9 - - - +
46B ASP* 1.3 65.4 + - - +
47B ILE* 3.9 22.6 + - + -
68B ILE* 4.1 7.2 - - + -
85B LEU* 3.6 22.5 - - + +
95B HIS* 4.0 1.4 - - - +
96B TYR* 2.9 31.7 + - + +
119B PHE* 3.6 19.3 - - + -
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Residues in contact with ASP 46 (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* 4.6 4.9 - - - +
16B GLU* 3.3 5.7 - - - +
17B ILE* 3.5 0.5 - - - -
18B ALA* 2.8 48.8 + - + +
20B VAL* 4.0 21.1 - - - +
44B GLU* 2.4 36.4 - - - +
45B ALA* 1.3 71.8 - - - +
47B ILE* 1.3 60.3 + - - +
48B HIS* 4.0 18.3 + - + +
94B PRO 5.1 0.3 - - - +
95B HIS* 3.6 8.4 - - - +
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Residues in contact with ILE 47 (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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15B MET* 3.7 33.0 - - + -
16B GLU 3.2 7.4 - - - +
17B ILE* 4.1 15.3 - - + -
45B ALA* 3.9 10.6 + - + +
46B ASP* 1.3 84.3 - - - +
48B HIS* 1.3 65.9 + - - +
62B TRP* 3.3 15.3 - - - +
63B MET* 3.1 22.2 + - + -
66B LEU* 3.7 19.5 - - + -
68B ILE* 3.4 33.0 - - + -
96B TYR* 4.5 5.8 - - + -
121B ILE* 4.2 20.2 - - + -
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Residues in contact with HIS 48 (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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61A PHE* 4.4 7.9 - + - -
15B MET* 3.3 2.6 - - - -
16B GLU* 2.8 42.3 + - + +
46B ASP* 4.0 17.4 + - + +
47B ILE* 1.3 88.5 + - - +
49B ALA* 1.3 63.7 + - - +
60B GLY* 3.3 27.8 - - - +
61B PHE 3.2 6.1 - - - +
62B TRP* 3.6 29.7 - + + +
63B MET* 4.0 6.1 - - - -
94B PRO* 4.6 8.8 + - - +
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Residues in contact with ALA 49 (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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14B GLY 3.6 5.6 - - - -
16B GLU* 5.8 0.2 - - - +
48B HIS* 1.3 74.5 - - - +
50B LEU* 1.3 63.3 + - - +
53B ASN* 4.0 5.6 - - - +
57B PHE* 3.7 29.8 - - + +
58B PRO 3.4 23.1 - - - +
59B GLU* 4.1 1.6 - - - +
60B GLY* 2.9 23.7 + - - -
61B PHE 2.9 11.4 + - - +
63B MET* 3.8 11.2 - - - -
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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