Contacts of the strand formed by residues 7 - 18 (chain F) in PDB entry 1R5I
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 PHE 7 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14E LEU* 3.6 3.6 - - - +
15E ASN* 3.0 45.6 + - + -
16E PRO* 5.3 1.1 - - + -
70E LEU* 3.3 10.5 - - + +
74E THR* 3.4 36.3 - - + +
79E TYR* 3.5 31.2 - + + -
80E THR 3.3 21.1 - - - -
81E PRO* 3.6 11.2 - - + -
5F PRO* 4.1 26.2 - - + -
6F ARG* 1.3 76.3 - - - +
8F LEU* 1.3 60.2 + - - +
32F TYR* 3.2 21.8 - - - +
33F ASN* 3.7 3.6 - - - -
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Residues in contact with LEU 8 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12E PHE* 4.1 13.2 - - + -
13E TYR 3.7 14.1 - - - +
14E LEU* 3.9 15.5 - - + -
70E LEU* 3.7 2.2 - - - +
82E ILE* 4.0 8.7 - - + -
113E THR* 3.9 20.2 - - - +
115E PRO* 3.7 26.7 - - + -
145E PHE* 4.0 6.1 - - + -
6F ARG 4.2 0.2 - - - -
7F PHE* 1.3 73.9 - - - +
9F TRP* 1.3 59.6 + - - +
10F GLN* 3.3 34.5 - - + +
32F TYR* 3.5 9.0 - - - -
33F ASN* 2.6 50.9 + - - +
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Residues in contact with TRP 9 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12E PHE* 3.1 4.7 - - - +
13E TYR* 3.0 35.5 + - + +
66E ASP* 3.8 42.2 + - + -
69E ASN* 3.9 20.5 - - + +
70E LEU* 3.4 26.5 - - + -
73E MSE 3.5 37.7 - - + -
8F LEU* 1.3 73.3 - - - +
10F GLN* 1.3 71.6 + - - +
11F LEU* 4.6 5.2 - - + +
30F CYS* 3.4 41.3 - - + -
31F ILE 3.6 8.7 - - - -
32F TYR* 4.0 19.1 - + + -
37F SER* 4.5 0.9 - - - -
61F TRP* 5.8 0.2 - + - -
313G THR* 5.3 0.2 + - - -
316G LEU* 4.0 24.0 - - + -
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Residues in contact with GLN 10 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11E GLU 3.4 6.5 - - - +
12E PHE* 3.8 15.7 - - + +
139E PRO* 5.7 0.9 - - - +
143E HIS* 3.2 30.3 + - - +
144E LEU 5.3 0.3 - - - +
145E PHE* 3.5 21.1 - - - -
8F LEU* 3.3 26.6 - - + +
9F TRP* 1.3 82.4 - - - +
11F LEU* 1.3 60.8 - - - +
12F LYS* 3.7 23.6 + - - -
30F CYS* 3.6 2.6 - - - -
31F ILE* 2.8 51.1 + - + +
33F ASN 3.5 10.3 + - - -
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Residues in contact with LEU 11 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9E GLN 4.5 0.2 - - - -
10E ALA* 3.6 0.7 - - - -
11E GLU* 2.9 45.6 + - + +
66E ASP* 3.9 10.1 - - - +
9F TRP* 4.6 7.2 - - + +
10F GLN* 1.3 74.3 - - - +
12F LYS* 1.3 69.4 + - - +
13F PHE* 3.5 37.5 - - + -
28F GLU* 4.5 10.5 - - + +
29F ARG 3.3 21.5 - - - +
30F CYS* 4.0 17.3 - - - -
313G THR* 3.2 35.0 - - - +
314G LEU 5.1 0.9 - - - +
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Residues in contact with LYS 12 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8E ILE* 4.5 14.8 - - + +
9E GLN 3.4 5.8 - - - +
10E ALA* 4.5 9.4 - - + -
11E GLU 5.5 0.4 - - - +
139E PRO* 3.8 23.8 - - + +
140E ARG 3.0 29.1 + - - +
141E GLU* 4.9 1.2 - - - +
143E HIS* 3.2 26.6 - - + +
144E LEU 5.5 0.2 + - - -
10F GLN* 3.7 22.6 + - + -
11F LEU* 1.3 82.2 - - - +
13F PHE* 1.3 63.5 - - - +
14F GLU* 4.0 15.3 - - + +
27F LEU 3.5 1.6 - - - +
28F GLU* 3.2 4.5 - - - +
29F ARG* 2.7 45.1 + - + +
31F ILE* 4.3 11.0 - - + -
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Residues in contact with PHE 13 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7E ILE 3.6 2.3 - - - +
8E ILE* 3.3 3.9 - - - -
9E GLN* 2.8 70.1 + - + +
11E GLU* 4.3 1.6 - - - -
11F LEU* 3.5 38.8 - - + -
12F LYS* 1.3 72.3 - - - +
14F GLU* 1.3 60.9 + - - +
26F LEU* 4.7 5.8 - - + -
27F LEU 3.5 3.6 - - - -
28F GLU* 3.2 41.5 - - + +
71F ARG* 4.2 4.0 - - - -
78F TYR* 3.3 24.3 + + + +
311G GLN* 3.3 33.2 - - + -
312G ASN 4.1 12.6 - - - -
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Residues in contact with GLU 14 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6E VAL* 4.7 0.2 - - + -
7E ILE 3.7 3.4 - - - -
8E ILE* 4.1 26.4 - - + +
141E GLU* 6.2 0.6 - - - +
12F LYS* 4.7 13.1 - - + +
13F PHE* 1.3 74.1 - - - +
15F CYS* 1.3 59.8 + - - +
16F HIS* 2.7 41.1 + - + +
25F ARG 3.5 1.4 - - - +
26F LEU* 3.3 8.9 - - - +
27F LEU* 2.7 53.3 + - + +
29F ARG* 3.0 41.0 + - - +
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Residues in contact with CYS 15 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6E VAL* 3.2 6.3 - - - +
7E ILE* 2.8 44.0 + - + +
14F GLU* 1.3 70.8 - - - +
16F HIS* 1.3 62.4 + - - +
17F PHE* 3.6 21.8 - - + -
24F VAL* 5.5 0.2 - - - -
25F ARG 3.6 3.8 - - - -
26F LEU* 3.7 1.3 - - - -
78F TYR* 3.5 24.9 - - - -
79F CYS* 2.1 53.6 - - - -
82F ASN* 5.6 1.3 - - - -
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Residues in contact with HIS 16 (chain F).
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* 2.8 33.3 + - - +
5E HIS 3.6 3.8 - - - -
6E VAL* 3.6 19.9 - - + +
8E ILE* 6.2 0.2 - - + -
14F GLU* 2.7 45.8 + - + +
15F CYS* 1.3 71.7 - - - +
17F PHE* 1.3 61.0 + - - +
18F PHE* 3.5 17.6 - + + -
24F VAL* 3.4 7.7 - - - +
25F ARG* 2.8 47.0 + - + +
27F LEU* 4.6 14.9 - - + +
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Residues in contact with PHE 17 (chain F).
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* 4.0 1.2 - - - +
4E GLU* 3.0 24.9 + - - +
5E HIS* 2.9 29.1 + - + +
7E ILE* 4.0 15.9 - - + -
15F CYS* 3.6 27.4 - - + -
16F HIS* 1.3 70.8 - - - +
18F PHE* 1.3 65.0 + - - +
20F GLY 3.4 11.4 - - - +
21F THR* 3.8 12.3 - - + -
23F ARG 3.7 1.8 - - - -
24F VAL* 3.5 28.0 - - + -
79F CYS* 3.1 41.7 - - + -
80F ARG* 4.1 1.3 - - - -
83F TYR* 3.5 42.6 - + + -
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Residues in contact with PHE 18 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1E ILE* 3.9 26.5 - - + +
2E LYS 3.1 26.5 - - - +
3E GLU* 3.4 27.8 - - + -
4E GLU 4.5 0.7 - - - +
16F HIS* 3.5 34.3 - + + -
17F PHE* 1.3 75.0 - - - +
19F ASN* 1.3 75.0 + - + +
20F GLY 3.5 1.0 + - - +
22F GLU 3.5 1.9 + - - -
23F ARG* 2.9 77.8 + - + +
25F ARG* 4.4 10.5 - - + -
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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