Contacts of the strand formed by residues 6 - 14 (chain E) in PDB entry 1RFU
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 6 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16A ARG* 3.6 33.1 - - - +
17A GLY 5.7 0.2 - - - +
277A LYS* 5.2 9.7 - - - +
4E GLU 4.0 0.8 + - - -
5E CYS* 1.3 73.2 - - - +
7E VAL* 1.3 64.5 + - - +
34E GLU* 3.2 35.2 - - + +
36E ASP* 3.0 28.0 + - - +
74E VAL 5.0 1.5 + - - -
76E GLN 3.2 26.1 + - - +
77E TYR* 3.5 24.0 - - + -
78E ASP* 3.0 40.4 + - - +
79E TYR* 3.2 5.7 + - - -
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Residues in contact with VAL 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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6E ARG* 1.3 80.1 - - - +
8E LEU* 1.3 63.4 + - - +
9E SER* 3.4 4.4 + - - +
28E LEU* 4.3 15.0 - - + -
33E PHE* 3.7 37.9 - - + -
34E GLU 2.8 9.1 + - - +
35E VAL* 3.6 4.1 - - + +
36E ASP 2.8 26.7 + - - -
77E TYR* 4.0 3.4 - - - -
79E TYR* 3.8 19.1 - - + -
81E LEU* 4.2 15.9 - - + -
242E LEU* 3.7 29.2 - - + -
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Residues in contact with LEU 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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15A VAL* 4.6 2.2 - - + -
7E VAL* 1.3 69.8 - - - +
9E SER* 1.3 58.9 + - - +
10E ILE* 3.7 20.2 + - + +
36E ASP* 3.4 16.2 - - + +
38E VAL* 4.0 24.7 - - + -
66E TYR* 5.2 5.8 - - + -
69E LEU* 5.1 2.7 - - + -
77E TYR* 3.4 48.3 - - + +
79E TYR 3.3 12.3 + - - +
80E VAL* 3.5 12.6 - - + +
81E LEU 3.1 20.7 + - - +
97E ILE* 4.7 9.9 - - + -
101E LEU* 4.2 16.8 - - + -
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Residues in contact with SER 9 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7E VAL* 3.4 4.8 + - - -
8E LEU* 1.3 73.3 - - - +
10E ILE* 1.3 61.4 + - - +
11E GLN* 2.8 21.9 + - - -
21E ASN* 2.8 26.6 + - - +
24E ALA* 4.6 1.1 - - - +
25E THR* 6.6 0.2 - - - -
28E LEU* 5.4 2.5 - - - -
35E VAL* 4.4 13.0 - - - -
36E ASP 2.8 12.3 + - - +
37E ALA* 3.5 1.7 - - - -
38E VAL 2.9 25.5 + - - +
81E LEU* 3.1 21.2 + - - +
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Residues in contact with ILE 10 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8E LEU* 4.1 28.9 - - + +
9E SER* 1.3 77.0 - - - +
11E GLN* 1.3 61.8 + - - +
38E VAL* 3.4 23.1 - - + +
40E SER* 4.9 0.7 - - - -
62E LEU* 4.8 10.5 - - + -
80E VAL* 5.5 1.6 - - + -
81E LEU 2.7 11.4 + - - +
82E THR* 3.4 9.4 - - + -
83E GLY* 2.9 24.6 + - - +
84E TYR 4.9 0.7 - - - +
85E THR* 5.5 1.1 + - - +
90E PHE* 3.5 36.8 - - + -
94E VAL* 4.3 27.8 - - + -
97E ILE* 5.3 7.2 - - + -
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Residues in contact with GLN 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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9E SER* 2.8 24.7 + - - +
10E ILE* 1.3 80.4 - - - +
12E SER* 1.3 60.7 + - - +
20E GLY* 3.8 11.7 - - - +
21E ASN* 3.0 27.5 + - - +
24E ALA* 3.3 24.7 - - - +
38E VAL 3.0 1.8 + - - -
39E ASN* 3.0 5.0 - - - -
40E SER* 2.8 30.8 + - - -
81E LEU* 3.9 11.8 - - - +
82E THR 4.2 2.5 - - - -
83E GLY* 3.6 19.5 - - - +
84E TYR 4.0 6.1 - - - +
113E ASP* 5.4 0.9 - - - +
235E ASP* 3.0 29.4 + - - +
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Residues in contact with SER 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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11E GLN* 1.3 75.9 - - - +
13E HIS* 1.3 58.0 + - - +
19E VAL* 4.1 0.9 - - - +
20E GLY* 3.0 12.9 + - - -
21E ASN* 2.6 34.1 + - - +
40E SER* 2.9 10.1 + - - -
41E VAL* 3.2 22.7 - - - -
84E TYR* 3.5 23.7 + - - +
4401E PLP 2.9 28.9 + - - +
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Residues in contact with HIS 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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13A HIS* 5.4 1.5 + + - -
37A ALA* 3.3 32.1 + - + -
39A ASN* 3.2 31.8 + - - -
12E SER* 1.3 75.1 - - - +
14E VAL* 1.3 75.6 + - - +
19E VAL 4.9 0.2 - - - -
21E ASN* 4.9 1.4 - - + +
22E ARG* 3.9 28.7 + - - +
39E ASN* 3.5 25.7 + - + +
41E VAL* 2.8 18.9 + - - +
42E GLN* 3.1 19.6 + - + -
43E PHE 2.9 24.1 + - - -
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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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13E HIS* 1.3 88.3 + - - +
15E VAL* 1.3 65.0 + - - +
16E ARG 3.1 22.4 - - - +
17E GLY 3.4 20.0 - - - +
19E VAL* 3.5 30.5 - - + +
22E ARG* 3.4 22.9 - - + +
43E PHE* 3.2 4.9 - - + +
45E ASN* 3.6 30.5 - - - +
46E HIS* 3.9 1.1 - - + +
4401E PLP 4.3 8.3 - - + -
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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