Contacts of the strand formed by residues 15 - 22 (chain A) in PDB entry 1L0Z
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 GLN 15 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12A TRP* 3.1 22.0 + - + +
13A PRO 4.3 4.5 - - - +
14A SER* 1.3 80.1 + - - +
16A ILE* 1.3 81.7 + - - +
31A GLY* 3.7 14.5 - - - -
32A GLY 3.6 12.7 + - - +
56A VAL 4.6 1.2 - - - +
57A VAL* 4.8 0.2 - - - -
58A GLY 4.7 8.7 + - - -
59A GLU 5.3 2.9 + - - +
108A TYR 5.5 0.3 - - - +
130A THR* 2.7 42.1 + - - +
131A GLY* 4.6 1.8 - - - -
132A TRP* 3.6 28.5 - - + -
145A LEU* 3.8 21.5 - - + -
190A GLY* 4.4 0.6 - - - -
191A PRO* 3.3 15.6 - - + +
193A HIS* 5.6 0.4 - - - -
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Residues in contact with ILE 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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14A SER 3.6 10.3 - - - +
15A GLN* 1.3 99.7 + - - +
17A SER* 1.3 74.1 + - - +
18A LEU* 3.7 9.6 - - + +
31A GLY* 3.5 2.1 - - - +
32A GLY* 2.9 46.7 + - - +
34A LEU* 4.1 12.8 - - + +
40A VAL* 3.8 23.1 - - + -
55A VAL* 4.0 17.7 - - + -
56A VAL 3.4 9.4 - - - +
57A VAL* 3.6 27.8 - - + -
132A TRP* 3.5 7.0 - - - -
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Residues in contact with SER 17 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A ILE* 1.3 74.8 - - - +
18A LEU* 1.3 59.1 + - - +
19A GLN* 2.9 30.9 + - - +
28A HIS* 2.8 25.3 + - - -
30A CYS 3.8 4.0 - - - -
54A ARG 3.7 0.9 - - - +
55A VAL* 3.5 3.3 - - - -
56A VAL* 2.9 39.9 + - - -
59A GLU* 4.3 2.0 - - - -
62A LEU* 3.7 6.1 - - - +
132A TRP* 3.8 17.6 - - - -
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Residues in contact with LEU 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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16A ILE* 3.7 11.3 - - + +
17A SER* 1.3 71.9 - - - +
19A GLN* 1.3 62.0 + - - +
28A HIS* 3.7 0.3 - - - -
29A THR* 2.8 27.0 + - + +
30A CYS* 2.8 28.9 + - + +
31A GLY 4.4 0.9 - - - +
42A THR* 4.2 8.7 - - - +
46A CYS* 4.0 27.1 - - + -
47A VAL* 4.1 16.2 - - + -
53A PHE* 3.9 32.1 - - + -
54A ARG 3.6 14.1 - - - +
55A VAL* 4.1 6.7 - - + -
74A VAL* 4.3 0.4 - - + -
97A LEU* 3.8 25.4 - - + -
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Residues in contact with GLN 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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17A SER* 2.9 33.0 + - - +
18A LEU* 1.3 75.6 - - - +
20A TYR* 1.3 61.9 + - - +
26A TRP* 3.7 10.0 - - + +
27A ALA 3.1 11.7 - - - +
28A HIS* 3.8 12.9 - - - +
29A THR* 4.3 0.7 - - - +
53A PHE* 3.2 9.3 - - - -
54A ARG* 2.9 71.8 + - + +
56A VAL* 3.6 18.0 - - + +
59A GLU* 4.0 5.3 + - - -
62A LEU* 3.8 17.2 + - - +
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Residues in contact with TYR 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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19A GLN* 1.3 74.8 - - - +
21A ARG* 1.3 75.4 - - - +
22A SER* 3.6 18.6 + - - -
26A TRP* 3.5 5.3 - - - -
27A ALA* 2.9 51.1 + - + +
28A HIS 4.6 2.2 - - - -
29A THR* 3.5 33.0 - - + -
49A ARG* 4.1 20.3 + - - -
51A LEU* 3.9 36.1 - - + -
52A THR 3.1 9.9 - - - +
53A PHE* 4.2 5.8 - - + -
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Residues in contact with ARG 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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20A TYR* 1.3 84.4 - - - +
22A SER* 1.3 61.4 + - - +
23A GLY 3.6 21.6 + - - +
24A SER* 5.0 9.0 - - - +
25A SER 3.6 8.1 - - - +
26A TRP* 3.5 38.9 - - + +
51A LEU* 5.4 4.7 - - - +
52A THR* 3.0 31.0 + - - +
275A BR 4.1 8.8 - - - +
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Residues in contact with SER 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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20A TYR* 3.6 21.1 + - - -
21A ARG* 1.3 75.5 - - - +
23A GLY* 1.3 62.6 + - - +
24A SER 3.4 0.2 + - - -
25A SER* 2.7 41.9 + - - -
27A ALA* 4.8 8.5 - - - -
275A BR 4.1 5.2 - - - -
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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