Contacts of the strand formed by residues 13 - 21 (chain E) in PDB entry 1E81
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 ALA 13 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6E PRO* 3.2 6.9 - - - +
7E ILE* 2.8 46.0 + - + +
11E ASP 3.1 1.0 - - - -
12E ASP* 1.3 81.9 - - - +
14E TYR* 1.3 71.2 + - - +
30E ASP* 4.0 18.8 - - - +
117E ILE* 4.2 8.1 - - + -
216E THR 6.0 0.2 - - - -
304E ASP* 4.3 4.3 - - - -
400E M91 4.2 11.7 - - + -
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Residues in contact with TYR 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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4E THR* 3.2 29.1 + - + +
5E THR 3.3 5.2 - - - +
6E PRO* 3.6 30.7 - - + -
11E ASP* 3.4 29.6 + - + +
13E ALA* 1.3 78.0 - - - +
15E ILE* 1.3 62.9 + - - +
16E THR* 4.9 0.2 + - - -
29E LEU 4.0 0.2 - - - +
30E ASP* 3.5 29.9 + - - +
31E PHE 4.3 2.6 + - - -
155E LEU* 3.8 28.9 - - + -
156E GLY 2.7 37.7 + - - -
159E ALA 4.3 0.7 - - - -
165E TYR* 5.4 3.1 - - + +
216E THR 5.3 2.6 + - - -
304E ASP* 3.7 27.1 - - + -
308E LYS* 3.6 13.2 - - - +
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Residues in contact with ILE 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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3E THR 4.1 1.0 - - - +
4E THR* 3.5 1.0 + - - -
5E THR* 2.8 45.9 + - + +
6E PRO 5.4 0.7 - - - +
7E ILE* 3.8 18.6 - - + -
14E TYR* 1.3 74.4 - - - +
16E THR* 1.3 62.3 + - - +
17E PRO* 4.3 2.8 - - - +
28E ASN* 4.0 35.2 - - + +
29E LEU 3.4 6.1 - - - +
116E THR* 3.4 33.2 - - + +
117E ILE* 3.7 22.0 - - + -
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Residues in contact with THR 16 (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 ALA* 3.4 35.0 - - + +
3E THR 3.5 14.6 - - - +
4E THR* 3.0 20.7 + - - -
14E TYR 4.9 0.3 + - - -
15E ILE* 1.3 73.2 - - - +
17E PRO* 1.3 69.4 - - - +
18E VAL* 3.4 4.9 + - - +
28E ASN* 4.3 1.3 - - - -
29E LEU 2.7 32.2 + - - +
31E PHE* 3.7 30.4 + - + +
165E TYR* 3.6 13.0 - - + -
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Residues in contact with PRO 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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2E ALA* 4.6 10.5 - - + +
3E THR* 3.3 21.5 - - - +
5E THR* 6.0 0.4 - - - +
15E ILE 4.3 2.2 - - - +
16E THR* 1.3 91.0 - - + +
18E VAL* 1.3 62.9 + - - +
19E GLN* 4.5 10.7 - - - +
26E THR* 4.1 14.4 - - + -
27E LEU 3.6 5.8 - - - +
28E ASN* 3.7 15.4 - - - +
90E SER 4.7 1.0 - - - +
91E VAL* 4.7 3.5 - - - +
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Residues in contact with VAL 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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16E THR 3.5 11.2 - - - +
17E PRO* 1.3 79.9 - - - +
19E GLN* 1.3 65.8 + - - +
20E ILE* 3.7 14.6 + - + +
25E GLN 3.4 2.6 - - - +
26E THR* 3.4 3.2 - - - +
27E LEU 2.8 36.5 + - - +
29E LEU* 4.0 21.5 - - + -
31E PHE* 3.8 26.9 - - + -
38E LEU* 5.9 0.2 - - + -
89E VAL* 3.6 28.7 - - + -
90E SER 3.7 7.2 - - - +
91E VAL* 4.2 7.2 - - + -
121E LEU* 4.3 4.3 - - + -
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Residues in contact with GLN 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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17E PRO* 4.5 8.2 - - - +
18E VAL* 1.3 76.9 - - - +
20E ILE* 1.3 61.4 + - - +
21E GLY 4.3 1.3 - - - +
24E ALA* 3.9 22.0 - - + -
25E GLN 3.9 3.1 - - - -
26E THR* 3.1 39.0 + - - +
88E THR 3.6 0.9 - - - +
89E VAL* 3.2 6.2 - - - +
90E SER* 2.8 60.6 + - - +
92E GLY 4.7 6.9 + - - -
93E GLY 5.4 1.2 + - - -
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Residues in contact with ILE 20 (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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18E VAL* 4.0 22.7 - - + +
19E GLN* 1.3 78.5 - - - +
21E GLY* 1.3 65.9 + - - +
25E GLN* 2.8 45.8 + - - +
27E LEU* 4.8 9.9 - - + -
29E LEU* 4.6 6.1 - - + -
38E LEU* 4.7 2.9 - - + -
40E VAL* 4.0 28.9 - - + -
56E TYR* 3.4 33.6 - - + -
87E ASP* 4.4 2.2 - - + -
88E THR 3.4 6.5 - - - +
89E VAL* 4.3 8.5 - - + -
101E VAL* 4.1 23.1 - - + -
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Residues in contact with GLY 21 (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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19E GLN* 5.3 0.7 - - - +
20E ILE* 1.3 78.0 + - - +
22E THR* 1.3 67.0 + - - +
23E PRO 3.3 5.6 - - - -
24E ALA* 3.5 12.8 + - - +
56E TYR* 4.8 0.2 - - - -
61E SER* 2.9 19.5 - - - -
63E THR* 3.8 0.2 - - - -
87E ASP* 3.2 15.2 + - - -
88E THR* 2.8 18.6 + - - +
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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