Contacts of the strand formed by residues 5 - 10 (chain A) in PDB entry 1LUA
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 LEU 5 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3A LYS* 3.6 17.0 - - + +
4A LYS* 1.3 74.9 - - - +
6A LEU* 1.3 60.5 + - - +
7A PHE* 4.0 15.5 - - + -
30A HIS* 3.6 26.2 - - + +
32A THR* 6.2 0.2 - - - +
53A ARG* 3.6 23.6 - - - +
60A SER 2.8 10.7 + - - +
61A THR* 3.3 7.0 - - - +
62A ALA 3.0 25.5 + - - +
268A PHE* 3.6 2.9 - - - -
21B VAL* 3.9 35.2 - - + -
24B TYR* 3.7 34.1 - - + -
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Residues in contact with LEU 6 (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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4A LYS 4.0 0.8 + - - -
5A LEU* 1.3 73.9 - - - +
7A PHE* 1.3 63.7 + - - +
8A GLN* 3.9 3.0 + - + -
19A ASP 5.6 1.8 - - - +
23A GLY* 4.6 4.9 - - - -
28A ALA* 4.1 5.4 - - + -
30A HIS 2.9 12.3 + - - +
31A ILE* 3.3 31.7 - - + +
32A THR* 2.9 25.5 + - - -
62A ALA* 3.5 23.8 - - + +
64A PHE* 4.0 26.9 - - + -
264A ILE* 4.2 17.7 - - + -
267A LEU* 4.0 23.1 - - + -
268A PHE* 4.1 12.1 - - + -
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Residues in contact with PHE 7 (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 LEU* 4.0 21.8 - - + -
6A LEU* 1.3 75.9 - - - +
8A GLN* 1.3 59.4 + - - +
9A PHE* 3.8 20.9 + - + -
32A THR* 3.5 31.0 - - + -
34A TYR* 4.1 11.0 - + - -
49A THR* 4.0 9.0 - - + -
61A THR* 3.9 19.7 - - + -
62A ALA 2.9 12.9 + - - +
63A ILE* 3.4 8.2 - - + +
64A PHE 2.9 26.3 + - - +
17B VAL* 3.6 23.8 - - + -
20B VAL* 3.8 22.9 - - + -
21B VAL* 3.7 32.3 - - + -
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Residues in contact with GLN 8 (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 LEU* 3.9 3.7 + - + -
7A PHE* 1.3 69.4 - - - +
9A PHE* 1.3 68.5 + - - +
10A ASP* 4.5 3.7 + - + +
15A PRO* 3.5 24.1 - - + +
16A SER* 3.2 30.5 + - - +
19A ASP* 3.7 18.4 + - - +
20A VAL* 3.3 20.8 - - - +
31A ILE* 3.8 17.6 - - + +
32A THR 3.0 7.2 + - - +
33A GLY* 3.4 9.6 - - - -
34A TYR 2.8 29.3 + - - +
64A PHE* 3.5 23.1 - - + -
66A GLY* 5.9 0.7 - - - +
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Residues in contact with PHE 9 (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 PHE* 4.0 26.0 - + + -
8A GLN* 1.3 77.3 - - - +
10A ASP* 1.3 59.9 + - - +
11A THR* 5.5 0.6 - - - +
34A TYR* 4.0 20.9 - + + -
37A VAL* 3.8 20.0 - - + -
42A VAL* 3.6 25.1 - - + -
45A TYR* 3.6 40.6 - + + -
46A VAL* 4.4 3.6 - - + -
49A THR* 5.1 0.9 - - + -
63A ILE* 3.8 42.8 - - + -
64A PHE 2.9 10.8 + - - +
65A VAL* 3.3 13.4 - - + +
66A GLY 3.0 23.8 + - - +
76A VAL* 4.7 1.6 - - + -
80A VAL* 4.4 4.9 - - + -
17B VAL* 4.8 1.1 - - + -
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Residues in contact with ASP 10 (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 GLN* 3.9 6.9 + - + -
9A PHE* 1.3 74.4 - - - +
11A THR* 1.3 65.1 + - - +
12A ASP* 2.7 33.3 + - - +
14A THR 3.9 11.8 - - - +
15A PRO* 3.8 15.0 - - + -
16A SER* 3.0 31.5 + - - -
19A ASP* 4.8 1.0 - - - +
34A TYR 2.9 15.2 + - - +
35A GLY 3.4 2.1 - - - -
36A ASN 3.3 7.6 + - - -
37A VAL* 3.2 19.7 + - - +
66A GLY* 3.4 4.3 - - - -
67A GLY* 3.2 22.8 + - - -
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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