Contacts of the strand formed by residues 41 - 49 (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 41 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6A ILE* 6.1 0.2 - - + -
21A TYR* 3.6 41.3 - - + -
22A LEU 3.2 9.0 - - - +
24A PRO* 3.8 7.8 - - - +
39A ALA* 3.9 2.4 - - - +
40A ASP* 1.3 83.9 - - - +
42A HIS* 1.3 62.7 + - - +
43A LEU* 4.5 12.6 - - + +
72A LEU* 5.2 3.6 - - + -
99A ASN* 3.3 5.4 - - - +
100A ILE* 2.9 46.8 + - + +
102A MET* 4.0 23.8 - - + -
152A PHE* 5.8 4.5 - - + -
154A TYR* 3.6 24.2 - - + +
158A PRO* 4.0 5.4 - - + -
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Residues in contact with HIS 42 (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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21A TYR* 3.2 5.0 - - - -
22A LEU* 2.8 40.8 + - + +
23A GLN 3.3 19.7 + - - +
24A PRO* 4.1 0.2 - - + -
25A ILE* 3.3 20.7 - - + +
33A ASP* 4.1 1.3 - - - -
41A ILE* 1.3 74.0 - - - +
43A LEU* 1.3 60.3 + - - +
44A GLU* 3.4 29.8 - - + -
88A MET* 3.9 4.0 - - + -
95A HIS* 3.1 3.6 + - - -
97A GLY* 3.6 7.6 - - - -
98A ALA* 3.4 27.1 - - - -
99A ASN* 2.8 22.4 + - - +
200A ZN 2.3 34.7 - - - -
132B HIS* 4.4 1.1 - + - -
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Residues in contact with LEU 43 (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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6A ILE* 3.4 33.9 - - + -
20A VAL 3.5 7.4 - - - +
21A TYR* 4.5 3.8 - - + -
41A ILE* 4.0 9.2 - - + +
42A HIS* 1.3 71.8 - - - +
44A GLU* 1.3 66.3 + - - +
70A TYR* 4.2 6.7 - - + -
72A LEU* 5.7 2.9 - - + -
85A LEU* 4.1 18.6 - - + +
97A GLY* 3.0 5.9 - - - -
98A ALA 2.9 36.6 + - - +
100A ILE* 3.7 27.8 - - + -
117A LEU* 3.9 31.9 - - + -
119A PHE* 4.3 7.6 - - + -
152A PHE* 6.1 0.7 - - + -
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Residues in contact with GLU 44 (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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3A GLU* 4.7 7.7 - - - +
19A ALA* 3.3 7.4 - - - +
20A VAL* 2.9 52.2 + - + +
22A LEU* 3.7 20.8 - - + +
42A HIS* 3.4 20.8 - - + -
43A LEU* 1.3 73.5 - - - +
45A ALA* 1.3 61.7 + - - +
46A ASP* 3.9 12.9 + - - +
90A ALA* 5.2 1.4 - - - +
92A ASP* 5.1 6.6 - - - +
95A HIS* 2.9 44.8 + - + +
96A TYR 3.3 5.6 - - - +
119A PHE* 4.2 4.7 - - - -
132B HIS* 4.0 5.4 - - - -
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Residues in contact with ALA 45 (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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18A ALA 3.5 5.4 - - - +
44A GLU* 1.3 71.6 - - - +
46A ASP* 1.3 64.2 + - - +
47A ILE* 3.8 23.4 + - + -
68A ILE* 4.4 2.2 - - + -
85A LEU* 3.7 16.1 - - + +
95A HIS* 3.9 2.6 - - - +
96A TYR* 2.9 34.9 + - + +
119A PHE* 3.5 28.3 - - + -
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Residues in contact with ASP 46 (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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3A GLU* 4.6 4.7 - - - +
16A GLU* 3.2 7.0 - - - +
17A ILE* 3.5 0.3 - - - -
18A ALA* 2.8 49.8 + - + +
20A VAL* 4.1 25.9 - - - +
44A GLU* 3.9 12.1 - - - +
45A ALA* 1.3 73.8 - - - +
47A ILE* 1.3 59.3 + - - +
48A HIS* 4.0 21.1 + - + +
94A PRO 5.0 0.9 - - - +
95A HIS* 3.9 16.3 - - - +
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Residues in contact with ILE 47 (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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15A MET* 3.7 37.0 - - + -
16A GLU 3.2 4.5 - - - +
17A ILE* 4.0 15.0 - - + -
45A ALA* 3.8 16.2 + - + +
46A ASP* 1.3 77.2 - - - +
48A HIS* 1.3 66.9 + - - +
62A TRP* 3.3 14.4 - - - -
63A MET* 3.0 28.8 + - + -
66A LEU* 3.8 12.3 - - + -
68A ILE* 3.4 34.1 - - + -
96A TYR* 4.1 8.1 - - + -
121A ILE* 4.1 16.6 - - + -
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Residues in contact with HIS 48 (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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15A MET* 3.2 3.1 - - - -
16A GLU* 2.8 48.3 + - + +
46A ASP* 4.0 20.0 - - + +
47A ILE* 1.3 89.6 + - - +
49A ALA* 1.3 65.9 + - - +
60A GLY* 3.2 27.6 - - - +
61A PHE 3.2 5.6 - - - +
62A TRP* 3.5 29.7 - + + +
63A MET* 3.8 5.8 - - - -
94A PRO* 4.6 6.2 + - - +
61B PHE* 4.5 8.7 - + - -
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Residues in contact with ALA 49 (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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14A GLY 3.4 6.5 - - - -
16A GLU* 5.7 0.6 - - - +
48A HIS* 1.3 74.3 - - - +
50A LEU* 1.3 63.3 + - - +
53A ASN* 4.1 4.5 - - - +
57A PHE* 3.6 30.1 - - + +
58A PRO 3.2 24.5 - - - +
59A GLU* 3.7 1.9 - - - +
60A GLY* 2.8 23.7 + - - -
61A PHE 2.9 9.9 + - - +
63A MET* 3.8 9.6 - - - -
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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