Contacts of the strand formed by residues 15 - 22 (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 MET 15 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10A LYS 3.7 0.5 - - - +
11A GLU* 3.2 4.3 - - - -
12A LEU* 2.8 31.5 + - - +
13A ASN* 3.6 20.6 - - + +
14A GLY* 1.3 82.9 - - - +
16A GLU* 1.3 59.5 + - - +
17A ILE* 4.1 5.4 - - + -
47A ILE* 3.7 28.5 - - + -
48A HIS 3.2 8.3 - - - +
50A LEU* 3.5 7.9 - - - +
63A MET* 3.8 34.3 - - + -
66A LEU* 4.3 7.2 - - - -
121A ILE* 5.2 1.6 - - + -
142A TRP* 5.8 0.2 - - + -
143A PHE* 3.2 39.7 - - + -
146A PHE* 4.0 15.5 - - + -
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Residues in contact with GLU 16 (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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9A PRO* 4.7 16.2 - - + +
10A LYS 3.4 7.0 - - - +
11A GLU* 4.4 14.1 - - + +
15A MET* 1.3 72.4 - - - +
17A ILE* 1.3 64.5 + - - +
18A ALA* 5.0 6.6 - - + +
46A ASP* 3.2 12.8 - - - +
47A ILE* 3.2 2.9 - - - +
48A HIS* 2.8 41.5 + - - +
49A ALA 5.7 0.2 - - - -
50A LEU* 3.7 17.3 - - + +
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Residues in contact with ILE 17 (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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9A PRO* 3.5 1.2 - - - +
10A LYS* 2.7 32.3 + - + +
12A LEU* 3.3 31.4 - - + -
15A MET* 4.1 11.7 - - + -
16A GLU* 1.3 77.8 - - - +
18A ALA* 1.3 59.5 + - - +
46A ASP 3.5 1.8 - - - -
47A ILE* 4.0 29.2 - - + -
119A PHE* 4.1 19.5 - - + -
121A ILE* 4.0 7.0 - - + -
146A PHE* 3.7 26.7 - - + -
148A VAL* 4.2 7.9 - - + -
150A TYR* 2.8 29.9 + - - +
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Residues in contact with ALA 18 (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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9A PRO* 4.1 22.2 - - + -
16A GLU* 5.2 7.6 - - + +
17A ILE* 1.3 76.0 - - - +
19A ALA* 1.3 62.2 + - - +
20A VAL* 5.7 2.2 - - + -
45A ALA* 3.5 4.9 - - - +
46A ASP* 2.8 46.8 + - + +
119A PHE* 4.3 1.4 - - - -
150A TYR* 4.1 3.4 - - - -
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Residues in contact with ALA 19 (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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5A PRO* 4.0 1.2 - - - +
6A ILE* 3.0 45.8 + - + +
18A ALA* 1.3 76.8 - - - +
20A VAL* 1.3 68.1 + - - +
44A GLU 3.3 5.8 - - - +
117A LEU* 3.9 10.5 - - + -
119A PHE* 3.8 26.2 - - + -
150A TYR* 4.2 10.9 - - + -
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Residues in contact with VAL 20 (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* 4.0 35.9 - - + +
4A VAL 3.2 14.1 - - - +
5A PRO* 4.4 7.9 - - + -
6A ILE* 3.7 6.3 - - - -
18A ALA* 5.6 3.1 - - + -
19A ALA* 1.3 80.8 - - - +
21A TYR* 1.3 63.2 + - - +
22A LEU* 4.4 3.1 - - + -
43A LEU* 3.5 6.2 - - - +
44A GLU* 2.9 59.7 + - + +
46A ASP* 4.1 15.0 + - - +
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Residues in contact with TYR 21 (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* 3.5 1.0 - - - -
4A VAL* 2.7 79.2 + - + +
6A ILE* 4.0 20.0 - - + -
20A VAL* 1.3 75.3 - - - +
22A LEU* 1.3 67.7 + - - +
41A ILE* 3.6 32.5 - - + -
42A HIS 3.2 12.1 - - - +
43A LEU* 4.5 1.1 - - - -
152A PHE* 3.9 25.6 - + - -
153A LYS 4.1 2.1 + - - -
154A TYR* 3.6 20.5 - + - -
155A THR* 3.5 32.4 + - - -
156A GLY 4.3 2.4 + - - -
158A PRO* 4.0 15.0 - - + -
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Residues in contact with LEU 22 (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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2A GLY 3.7 14.8 - - - +
3A GLU* 4.4 14.8 - - + +
20A VAL* 4.4 5.4 - - + -
21A TYR* 1.3 82.0 - - - +
23A GLN* 1.3 94.9 + - - +
25A ILE* 4.2 11.9 - - + -
41A ILE* 3.2 10.7 - - - +
42A HIS* 2.8 40.8 + - + +
44A GLU* 3.7 34.5 - - + +
158A PRO* 3.9 8.7 - - - -
132B HIS* 5.5 0.7 - - + -
137B THR* 4.2 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