Contacts of the helix formed by residues 2 - 12 (chain A) in PDB entry 5X11
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 2 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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0A PRO* 3.6 23.8 - - + +
1A MET* 1.3 79.0 - - - +
3A VAL* 1.3 64.8 + - - +
4A LEU* 3.2 3.8 - - - -
5A LYS* 3.1 42.9 + - + +
6A TYR* 3.4 12.8 - - + -
44A GLU* 2.6 31.5 + - - -
47A LYS* 3.1 34.9 - - - +
48A LEU* 3.8 2.8 - - - +
51A GLU* 3.3 33.7 + - - -
53A PHE* 5.6 0.2 - - - -
15J A 2.8 35.0 + - - +
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Residues in contact with VAL 3 (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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1A MET* 3.2 23.8 + - + -
2A ARG* 1.3 75.8 - - - +
4A LEU* 1.3 57.0 + - - +
6A TYR* 3.0 10.1 + - - +
7A ALA* 2.9 25.2 + - - +
34A TRP* 3.4 42.6 - - + -
83A TRP* 4.9 1.6 - - + -
97B GLU* 4.0 27.6 - - + +
100B LEU* 3.5 25.8 - - + -
15J A 4.7 0.2 + - - -
16J T 5.8 1.5 + - - +
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Residues in contact with LEU 4 (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 ARG 3.2 1.2 - - - -
3A VAL* 1.3 79.0 - - - +
5A LYS* 1.3 61.3 + - - +
7A ALA* 4.2 4.3 - - + -
8A ILE* 3.2 34.2 + - + +
26A PHE* 4.3 14.6 - - + -
34A TRP* 4.7 9.9 - - - +
36A ALA* 3.7 23.3 - - + -
40A GLN* 3.5 58.1 - - + +
41A ILE* 4.4 2.7 - - + +
44A GLU* 4.0 23.6 - - + +
16J T 4.4 7.9 + - - +
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Residues in contact with LYS 5 (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 ARG* 3.1 44.6 + - + +
4A LEU* 1.3 77.9 - - - +
6A TYR* 1.3 88.2 + - + +
8A ILE* 3.4 4.5 + - - +
9A LEU* 3.0 37.9 + - + +
44A GLU* 3.4 23.9 + - - +
48A LEU* 3.5 19.7 - - + -
53A PHE* 4.1 15.7 - - + -
79A GLU* 3.1 36.6 + - - -
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Residues in contact with TYR 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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1A MET 3.6 17.9 - - - -
2A ARG* 3.4 20.9 - - + -
3A VAL* 3.0 7.4 + - - +
5A LYS* 1.3 110.7 + - + +
7A ALA* 1.3 66.1 + - - +
9A LEU* 4.3 11.6 - - + +
10A GLY* 3.0 18.0 + - - -
79A GLU* 3.5 25.6 + - + -
80A LEU* 4.3 3.4 - - + +
83A TRP* 3.4 73.5 - + + -
86A ARG* 4.4 13.0 + - - -
104B PHE* 3.6 10.6 - - - -
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Residues in contact with ALA 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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3A VAL 2.9 12.3 + - - +
4A LEU* 3.7 12.6 - - - +
5A LYS 3.3 0.2 - - - -
6A TYR* 1.3 76.2 - - - +
8A ILE* 1.3 58.3 + - - +
11A LEU* 3.0 35.2 + - - +
26A PHE* 3.8 24.9 - - + -
34A TRP* 4.4 6.1 - - + -
100B LEU* 4.0 21.5 - - + +
104B PHE* 3.3 12.4 - - - -
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Residues in contact with ILE 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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4A LEU* 3.2 30.3 + - + +
5A LYS 3.7 3.6 - - - +
7A ALA* 1.3 74.5 - - + +
9A LEU* 1.3 67.0 + - - +
10A GLY 3.1 1.3 - - - -
11A LEU* 2.9 17.7 + - - +
12A LEU* 3.0 27.7 + - + +
22A ILE* 4.2 20.2 - - + -
26A PHE* 5.2 0.7 - - + -
41A ILE* 4.4 12.8 - - + -
44A GLU* 3.7 29.6 - - + -
45A LEU* 3.8 29.6 - - + -
48A LEU* 3.9 14.6 - - + -
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Residues in contact with LEU 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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5A LYS* 3.0 30.4 + - + +
6A TYR* 4.3 13.7 - - + +
8A ILE* 1.3 75.2 - - - +
10A GLY* 1.3 61.1 + - - +
12A LEU* 3.3 12.8 + - - +
13A ARG 3.4 8.5 + - - -
48A LEU* 4.1 14.6 - - + -
53A PHE* 4.0 14.6 - - + -
54A ILE* 3.8 27.4 - - + -
72A LEU* 3.7 24.3 - - + +
76A GLY* 3.8 18.4 - - - +
79A GLU* 3.9 23.1 - - + -
80A LEU* 3.7 17.5 - - + +
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Residues in contact with GLY 10 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6A TYR 3.0 12.4 + - - -
9A LEU* 1.3 74.7 - - - +
11A LEU* 1.3 62.8 - - - +
13A ARG* 3.0 30.8 + - - -
80A LEU* 3.7 20.3 - - - +
104B PHE* 3.3 26.7 - - - -
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Residues in contact with LEU 11 (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 ALA 3.0 22.2 + - - +
8A ILE* 2.9 8.3 + - - +
10A GLY* 1.3 75.0 - - - +
12A LEU* 1.3 57.5 + - - +
13A ARG* 3.4 9.1 + - - +
14A LYS* 4.8 2.8 + - - +
15A GLY 4.6 0.7 - - - +
17A LEU* 3.1 28.8 - - + +
22A ILE* 4.1 19.5 - - + -
25A TYR* 3.8 37.0 - - + -
26A PHE* 3.7 32.5 - - + -
30A LEU* 3.9 16.2 - - + -
103B TYR* 4.0 13.7 - - + -
104B PHE* 3.4 6.0 - - + -
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Residues in contact with LEU 12 (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 ILE* 3.0 32.6 + - + +
9A LEU* 3.3 8.5 + - - +
10A GLY 3.1 0.6 - - - -
11A LEU* 1.3 76.1 - - - +
13A ARG* 1.3 62.5 + - - +
14A LYS 3.1 4.4 + - - -
15A GLY* 3.2 18.6 + - - +
17A LEU* 3.6 33.0 - - + +
22A ILE* 4.4 8.1 - - + -
54A ILE* 3.8 30.3 - - + -
70A TYR* 3.6 38.6 - - + +
71A THR* 5.9 0.5 - - - +
72A LEU* 3.5 24.4 + - + +
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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