Contacts of the helix formed by residues 3 - 19 (chain E) in PDB entry 5ITX
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 GLU 3 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2E GLY* 1.3 72.7 - - - -
4E GLY* 1.3 68.9 + - - +
5E PRO* 3.2 5.8 - - + -
6E GLU* 2.8 18.7 + - - +
7E LEU* 3.3 11.9 + - - +
54E LYS* 3.8 7.9 - - - +
173E GLY 3.9 2.7 - - - +
175E GLY* 1.3 64.5 + - - +
176E ASN 2.9 2.0 - - - -
177E TYR* 2.8 53.6 + - + -
178E LEU* 3.3 6.5 + - + -
297F CTG 3.1 22.7 + - - +
298F G 3.2 1.3 - - - +
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Residues in contact with GLY 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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3E GLU* 1.3 69.7 - - - +
5E PRO* 1.4 68.5 - - - +
7E LEU* 3.2 5.5 + - - +
8E HIS* 3.1 18.0 + - - +
53E GLY* 3.6 21.5 - - - +
54E LYS* 4.5 2.0 - - - +
136E CYS* 6.5 0.2 - - - -
137E VAL* 6.3 1.3 - - - -
138E LEU* 4.5 9.7 - - - +
173E GLY* 2.8 29.4 + - - -
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Residues in contact with PRO 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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3E GLU 3.5 1.8 - - - -
4E GLY* 1.4 80.6 - - - +
6E GLU* 1.3 62.5 + - - +
8E HIS* 2.7 29.6 + - + +
9E LEU* 2.7 22.0 + - + +
138E LEU* 4.4 6.2 - - + -
177E TYR* 3.4 17.3 - - - +
178E LEU* 3.6 15.0 - - + -
233E PRO* 3.6 31.6 - - + +
236E VAL* 3.4 24.7 - - + -
237E VAL* 4.5 6.3 - - + +
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Residues in contact with GLU 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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2E GLY* 3.7 13.7 - - - -
3E GLU 2.8 17.1 + - - +
5E PRO* 1.3 79.6 - - - +
7E LEU* 1.3 64.8 + - + +
9E LEU* 3.8 10.4 - - + +
10E ALA* 3.0 24.3 + - - +
79E PHE* 5.0 6.3 - - + -
177E TYR* 2.9 23.1 + - - -
236E VAL* 4.3 3.1 - - - +
242E ARG* 4.7 15.0 + - - +
256E PHE* 4.2 6.4 - - - -
297F CTG 3.2 33.7 + - - +
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Residues in contact with LEU 7 (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 GLY* 4.0 17.5 - - - +
3E GLU 3.4 21.8 - - - +
4E GLY 3.5 6.5 - - - +
5E PRO 3.0 0.6 - - - -
6E GLU* 1.3 83.3 - - + +
8E HIS* 1.3 64.8 + - - +
10E ALA* 3.3 11.0 + - - +
11E SER* 3.4 12.6 + - - -
51E ALA* 4.6 3.4 - - + +
53E GLY 3.8 8.3 - - - +
54E LYS* 3.8 28.7 - - + +
55E GLU* 4.1 11.2 - - - +
56E LEU* 4.0 20.2 - - + +
77E PHE 5.2 0.4 - - - +
79E PHE* 3.4 47.6 - - + +
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Residues in contact with HIS 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 GLY 3.1 4.0 + - - +
5E PRO 2.7 13.3 + - - +
7E LEU* 1.3 74.1 - - - +
9E LEU* 1.3 63.4 + - - +
11E SER* 3.1 15.0 + - - -
12E GLN* 3.3 38.3 + - + +
51E ALA* 3.6 25.4 - - + +
138E LEU* 3.8 24.3 - - + +
139E GLN* 3.4 34.2 + - - -
237E VAL* 3.9 19.8 - - + +
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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 PRO 2.7 24.3 + - - +
6E GLU* 3.8 9.2 - - - +
8E HIS* 1.3 71.9 - - - +
10E ALA* 1.3 63.8 + - - +
12E GLN* 3.1 25.5 + - + +
13E PHE* 3.1 20.3 + - - +
236E VAL* 3.8 27.1 - - + +
237E VAL* 3.7 27.4 - - + +
239E LEU* 5.8 3.1 - - + -
241E GLY 5.1 13.9 - - - +
242E ARG* 5.4 11.2 - - - +
244E TYR* 4.3 19.3 - - + +
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Residues in contact with ALA 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 GLU 3.0 14.2 + - - +
7E LEU 3.3 9.4 + - - +
9E LEU* 1.3 75.2 - - - +
11E SER* 1.3 58.9 + - - +
13E PHE* 3.0 8.4 + - - +
14E VAL* 2.9 31.2 + - - +
56E LEU* 4.1 5.6 - - + -
79E PHE* 4.0 27.4 - - + -
84E SER* 6.0 0.2 - - - -
85E PHE* 4.4 11.4 - - + +
244E TYR* 4.3 14.0 + - - +
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Residues in contact with SER 11 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7E LEU 3.4 5.4 + - - -
8E HIS* 3.1 13.3 + - - -
10E ALA* 1.3 75.3 - - - +
12E GLN* 1.3 63.5 + - - +
14E VAL* 3.8 2.4 - - - +
15E ASN* 3.0 32.6 + - - -
49E ALA* 3.5 28.5 - - - -
50E SER 2.6 33.3 + - - -
51E ALA* 3.7 4.7 - - - +
56E LEU* 4.1 5.7 - - - +
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Residues in contact with GLN 12 (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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8E HIS* 3.3 40.6 + - + +
9E LEU* 3.1 22.4 + - + +
11E SER* 1.3 76.4 + - - +
13E PHE* 1.3 57.8 + - - +
15E ASN* 3.9 3.5 - - - +
16E GLU* 2.9 55.2 + - - +
237E VAL* 3.8 14.1 + - - +
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Residues in contact with PHE 13 (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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9E LEU 3.1 4.8 + - - +
10E ALA* 3.0 10.8 + - - +
12E GLN* 1.3 75.4 - - - +
14E VAL* 1.3 66.0 + - + +
16E GLU* 3.4 3.8 - - - -
17E ALA* 2.7 54.8 + - + +
85E PHE* 3.8 28.0 - - + -
86E GLN* 4.8 0.9 - - - -
87E LEU* 4.1 31.9 - - + -
112E LEU* 4.9 6.3 - - + -
244E TYR* 3.3 70.0 - + + -
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Residues in contact with VAL 14 (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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10E ALA 2.9 21.2 + - - +
11E SER* 3.8 6.1 - - - +
13E PHE* 1.3 85.9 - - + +
15E ASN* 1.3 54.9 + - - +
17E ALA* 3.3 2.0 + - - -
18E CYS* 2.7 49.1 + - + +
47E ILE* 4.3 12.3 - - + -
48E SER* 4.6 0.9 - - - -
49E ALA* 3.9 24.7 - - + +
56E LEU* 5.7 0.4 - - + -
58E LEU* 4.2 13.9 - - + -
85E PHE* 4.2 33.4 - - + -
112E LEU* 4.9 9.0 - - + -
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Residues in contact with ASN 15 (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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11E SER 3.0 17.5 + - - +
12E GLN* 3.9 4.6 - - - +
14E VAL* 1.3 75.2 - - - +
16E GLU* 1.3 61.5 + - + +
17E ALA 2.9 6.9 + - - -
19E ARG* 2.8 43.7 + - + +
47E ILE 4.5 2.2 - - - +
48E SER* 3.1 27.4 - - - -
49E ALA 2.5 34.4 + - - +
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Residues in contact with GLU 16 (chain E).
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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12E GLN* 2.9 54.4 + - - +
13E PHE* 3.4 5.1 - - - +
15E ASN* 1.3 74.4 - - + +
17E ALA* 1.3 55.7 + - - +
19E ARG* 3.3 28.5 + - - +
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Residues in contact with ALA 17 (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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13E PHE* 2.7 44.4 + - + +
14E VAL* 3.9 2.2 - - - +
16E GLU* 1.3 76.9 - - - +
18E CYS* 1.3 63.1 + - - +
19E ARG 3.7 1.6 - - - -
20E ALA* 4.6 5.6 + - - +
21E LEU* 3.8 24.8 + - - +
87E LEU* 4.7 14.9 - - + +
112E LEU* 6.2 0.2 - - + -
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Residues in contact with CYS 18 (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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14E VAL* 2.7 28.3 + - - +
15E ASN 3.7 0.2 - - - -
17E ALA* 1.3 80.6 - - - +
19E ARG* 1.3 65.1 + - - +
20E ALA 3.2 1.7 + - - +
21E LEU* 3.5 21.7 - - - +
23E PHE* 3.8 33.7 - - + -
46E ARG* 4.6 2.9 - - - -
47E ILE* 3.6 32.6 + - + +
87E LEU* 6.0 2.0 - - - -
112E LEU* 4.2 22.2 - - - -
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Residues in contact with ARG 19 (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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15E ASN* 2.8 25.3 + - - +
16E GLU* 3.3 39.4 + - - +
17E ALA 3.7 0.4 - - - -
18E CYS* 1.3 73.8 - - - +
20E ALA* 1.3 61.0 + - - +
46E ARG* 3.7 20.9 + - - +
47E ILE 4.5 2.2 + - - -
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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