Contacts of the helix formed by residues 2 - 12 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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0E PRO* 3.9 24.7 - - + +
1E MET* 1.3 73.1 - - - +
3E VAL* 1.3 64.8 + - - +
4E LEU* 3.3 3.4 - - - -
5E LYS* 3.1 43.0 + - + +
6E TYR* 3.5 8.2 + - + -
44E GLU* 2.5 35.3 + - - -
47E LYS* 3.7 29.8 - - - +
48E LEU* 4.6 1.2 - - - +
51E GLU* 2.8 40.9 + - - -
15N A 2.8 38.3 + - - +
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Residues in contact with VAL 3 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1E MET* 3.3 33.2 - - + +
2E ARG* 1.3 71.1 - - - +
4E LEU* 1.3 51.7 + - - +
6E TYR* 2.9 10.6 + - - +
7E ALA* 2.8 33.6 + - + +
34E TRP* 3.6 49.1 - - + -
83E TRP* 4.8 18.6 - - + +
15N A 4.8 0.4 + - - -
16N T 5.8 0.2 - - - +
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Residues in contact with LEU 4 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2E ARG 3.3 1.0 - - - -
3E VAL* 1.3 76.3 - - - +
5E LYS* 1.3 64.2 + - - +
7E ALA* 3.1 4.4 + - + -
8E ILE* 2.8 39.8 + - + +
26E PHE* 4.1 13.5 - - + -
34E TRP* 4.7 10.4 - - - +
36E ALA* 3.8 23.8 - - + -
40E GLN* 3.5 51.1 - - + +
41E ILE* 4.5 2.5 - - + -
44E GLU* 4.0 23.3 - - + +
16N T 4.6 12.8 + - - +
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Residues in contact with LYS 5 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2E ARG* 3.1 39.0 + - + +
4E LEU* 1.3 78.5 - - - +
6E TYR* 1.3 79.2 + - + +
8E ILE* 3.3 2.6 + - - +
9E LEU* 3.0 36.8 + - + +
44E GLU* 3.7 21.4 + - - +
48E LEU* 3.6 22.7 - - + +
53E PHE* 3.7 23.1 - - - -
79E GLU* 2.9 44.4 + - - -
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Residues in contact with TYR 6 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1E MET 4.0 15.9 - - - -
2E ARG* 3.5 14.1 + - + -
3E VAL* 2.9 8.2 + - - +
5E LYS* 1.3 93.6 + - + +
7E ALA* 1.3 65.2 + - - +
9E LEU* 4.1 13.5 - - + +
10E GLY* 3.1 19.9 + - - -
79E GLU* 2.9 45.5 + - + -
80E LEU* 4.1 8.9 - - - +
83E TRP* 3.4 75.9 - + + +
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Residues in contact with ALA 7 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3E VAL* 2.8 18.9 + - + +
4E LEU* 3.4 13.5 - - + +
6E TYR* 1.3 74.0 - - - +
8E ILE* 1.3 61.4 + - - +
10E GLY* 3.8 0.7 - - - -
11E LEU* 3.1 29.8 + - - +
26E PHE* 3.9 26.7 - - + -
30E LEU* 5.7 3.3 - - + +
34E TRP* 4.5 11.2 - - + -
83E TRP* 5.2 2.8 - - - -
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Residues in contact with ILE 8 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4E LEU* 2.8 30.7 + - + +
5E LYS 3.7 3.1 - - - +
7E ALA* 1.3 73.9 - - + +
9E LEU* 1.3 65.4 + - - +
10E GLY 3.3 0.9 + - - -
11E LEU* 3.3 15.8 + - - +
12E LEU* 3.3 31.0 + - + +
22E ILE* 3.9 24.2 - - + -
26E PHE* 5.0 0.4 - - + -
41E ILE* 3.9 27.4 - - + +
44E GLU* 3.9 30.1 - - + -
45E LEU* 3.9 12.8 - - + -
48E LEU* 4.0 13.9 - - + -
54E ILE* 5.0 0.2 - - + -
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Residues in contact with LEU 9 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5E LYS* 3.0 27.9 + - + +
6E TYR* 4.1 15.0 - - + +
7E ALA 3.4 0.2 - - - -
8E ILE* 1.3 76.3 - - - +
10E GLY* 1.3 60.0 + - - +
12E LEU* 3.3 8.5 + - - -
13E ARG 3.5 5.5 + - - -
48E LEU* 4.5 11.0 - - + -
53E PHE* 3.9 17.5 - - + -
54E ILE* 3.8 17.9 - - + -
72E LEU* 3.4 35.6 - - + +
76E GLY* 3.9 6.7 - - - +
79E GLU* 3.9 35.0 - - + -
80E LEU* 3.8 21.7 - - + +
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Residues in contact with GLY 10 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6E TYR 3.1 18.2 + - - -
7E ALA 3.8 0.9 - - - -
9E LEU* 1.3 72.9 - - - +
11E LEU* 1.3 58.6 + - - +
12E LEU 3.0 6.7 + - - -
13E ARG* 2.9 37.0 + - - -
80E LEU* 3.9 19.5 - - - +
83E TRP* 6.2 0.2 - - - -
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Residues in contact with LEU 11 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7E ALA 3.1 22.3 + - - +
8E ILE* 3.3 7.2 + - - +
10E GLY* 1.3 74.3 - - - +
12E LEU* 1.3 57.6 + - - +
13E ARG* 3.5 10.6 + - - +
14E LYS* 4.9 2.6 + - - +
15E GLY 4.7 0.7 - - - +
17E LEU* 2.9 29.4 - - + +
22E ILE* 3.8 32.1 - - + -
25E TYR* 3.8 43.0 - - + -
26E PHE* 4.0 19.7 - - + -
30E LEU* 4.1 18.2 - - + -
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Residues in contact with LEU 12 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8E ILE* 3.4 31.0 - - + +
9E LEU 3.3 8.0 + - - +
10E GLY 3.0 1.2 - - - -
11E LEU* 1.3 78.7 - - - +
13E ARG* 1.3 61.9 + - - +
14E LYS 3.2 4.8 + - - -
15E GLY* 3.4 17.7 + - - +
17E LEU* 3.5 31.2 - - + +
22E ILE* 4.8 5.2 - - + -
54E ILE* 3.8 29.6 - - + -
70E TYR* 3.4 39.0 - - + +
71E THR* 5.5 0.6 - - - +
72E LEU* 3.7 22.2 + - + +
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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