Contacts of the strand formed by residues 21 - 29 (chain A) in PDB entry 1L7R
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 ARG 21 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13A MET* 3.7 48.1 + - + +
14A VAL 3.2 6.5 - - - +
15A PRO* 3.9 20.9 - - + -
19A GLY 3.9 7.9 - - - +
20A VAL* 1.3 76.3 - - - +
22A LEU* 1.3 64.3 + - - +
81A GLU* 2.8 63.2 + - - +
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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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12A VAL 3.5 1.0 - - - +
13A MET* 3.6 2.4 - - - -
14A VAL* 2.8 36.5 + - - +
16A MET* 3.8 31.6 - - + -
20A VAL* 4.5 2.9 - - + -
21A ARG* 1.3 78.2 - - - +
23A ALA* 1.3 62.5 + - - +
24A VAL* 4.7 0.2 - - - -
41A ARG* 3.8 17.9 - - - +
72A GLN* 3.5 35.4 - - - +
73A ASP 4.1 4.3 - - - +
75A ARG* 3.5 34.5 - - + +
80A SER* 3.3 13.9 - - - +
81A GLU 4.1 4.3 - - - +
93A ASP* 3.8 7.6 - - + +
97A THR* 4.5 0.2 - - - +
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Residues in contact with ALA 23 (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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11A ASN* 3.9 3.4 - - - +
12A VAL 3.7 4.5 - - - -
13A MET* 3.7 13.7 - - - +
22A LEU* 1.3 72.3 - - - +
24A VAL* 1.3 61.4 + - - +
46A LYS* 3.5 9.9 - - - +
72A GLN* 3.4 2.8 - - - +
73A ASP* 2.9 28.3 + - - +
79A ALA* 3.3 44.9 - - + +
80A SER* 2.7 12.3 + - - +
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Residues in contact with VAL 24 (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 ALA 4.1 0.2 - - - +
11A ASN 3.3 5.4 + - - -
12A VAL* 2.8 55.0 + - + +
14A VAL* 3.9 20.9 - - + -
22A LEU 4.2 0.4 - - - +
23A ALA* 1.3 80.6 - - - +
25A ASP* 1.3 64.2 + - - +
26A LEU* 3.9 18.4 - - + -
46A LYS* 3.8 0.7 - - - -
70A VAL* 3.8 15.0 - - + -
71A ILE 3.1 9.0 - - - +
72A GLN* 3.5 33.9 - - + +
97A THR* 5.2 2.0 - - + -
100A TRP* 4.6 1.8 - - + -
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Residues in contact with ASP 25 (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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8A VAL* 4.9 4.3 - - + -
9A ALA 3.3 5.2 - - - +
10A SER* 3.4 8.2 - - - -
11A ASN 3.1 16.5 + - - -
24A VAL* 1.3 72.4 - - - +
26A LEU* 1.3 63.3 + - - +
27A TYR* 3.9 25.9 + - + -
46A LYS* 2.9 35.8 + - - +
47A PHE* 3.1 29.8 - - - -
69A VAL 3.7 1.7 - - - +
70A VAL* 3.4 6.2 - - - -
71A ILE* 2.8 32.4 + - + +
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Residues in contact with LEU 26 (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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7A SER 3.3 2.3 - - - +
8A VAL* 3.1 6.7 - - - -
9A ALA* 2.8 36.5 + - + +
12A VAL* 3.7 28.9 - - + -
24A VAL* 3.9 18.6 - - + -
25A ASP* 1.3 72.6 - - - +
27A TYR* 1.3 62.7 + - - +
28A ARG* 3.7 35.8 + - + +
69A VAL 3.8 1.1 - - - -
70A VAL* 3.7 27.1 - - + -
100A TRP* 4.3 9.2 - - + -
106A TRP* 3.8 27.8 - - + +
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Residues in contact with TYR 27 (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 TYR* 4.3 4.3 - + + -
7A SER 3.4 6.3 - - - -
8A VAL* 3.5 33.3 - - + +
25A ASP* 3.9 27.9 + - + -
26A LEU* 1.3 72.5 - - - +
28A ARG* 1.3 61.6 + - - +
29A PRO* 4.0 0.7 - - - +
46A LYS 4.8 1.0 + - - -
47A PHE* 5.5 1.2 + - - -
49A VAL* 3.9 19.6 - - - +
59A TRP* 3.7 27.1 - + - -
60A LEU* 4.3 12.3 - - + -
63A VAL* 4.0 22.1 - - + +
67A TYR 4.1 1.6 - - - +
68A ALA* 3.2 5.4 - - - +
69A VAL* 2.8 49.1 + - + +
71A ILE* 3.6 19.7 - - + +
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Residues in contact with ARG 28 (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 TYR* 3.8 3.4 - - - -
7A SER* 2.9 51.3 + - - +
9A ALA* 3.8 23.6 - - - +
26A LEU* 3.7 26.5 + - + +
27A TYR* 1.3 79.1 - - - +
29A PRO* 1.3 72.2 - - + +
30A ASP* 3.6 0.5 + - - -
35A VAL* 6.1 0.4 - - + -
63A VAL* 4.7 0.2 - - - +
68A ALA* 4.2 13.0 - - + -
106A TRP* 3.4 54.9 - - + +
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Residues in contact with PRO 29 (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 ASN 3.6 9.0 - - - +
6A TYR* 3.8 4.4 - - + -
27A TYR 4.0 0.2 - - - +
28A ARG* 1.3 89.1 - - + +
30A ASP* 1.3 70.4 + - - +
31A ALA* 3.1 9.3 + - + +
35A VAL* 4.0 18.2 - - + -
63A VAL* 3.6 18.6 - - + +
66A GLY* 3.6 30.3 - - - +
67A TYR 3.4 17.5 - - - +
68A ALA* 3.7 10.1 - - + -
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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