Contacts of the strand formed by residues 51 - 60 (chain F) in PDB entry 5IRC
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 LYS 51 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4F ILE* 4.1 22.0 - - + -
46F ILE 3.7 0.9 - - - +
47F GLU* 3.3 4.4 - - - -
48F VAL 2.9 32.8 + - - +
49F ASP* 3.1 8.6 - - + +
50F GLY* 1.3 81.0 - - - +
52F GLN* 1.3 63.7 + - - +
53F VAL* 3.9 2.7 + - - +
179F LEU* 3.9 22.9 - - + -
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Residues in contact with GLN 52 (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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4F ILE* 3.4 28.6 + - - +
45F ASP* 5.7 3.6 - - - +
46F ILE 3.6 4.0 - - - +
47F GLU* 4.5 14.1 - - + -
50F GLY 4.1 3.7 + - - +
51F LYS* 1.3 74.7 - - - +
53F VAL* 1.3 61.5 + - - +
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Residues in contact with VAL 53 (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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4F ILE* 3.2 14.6 - - + +
6F LYS* 3.9 26.2 - - + -
45F ASP* 3.5 8.6 - - - +
46F ILE* 2.8 46.7 + - + +
51F LYS 4.5 4.0 - - - +
52F GLN* 1.3 78.5 - - - +
54F GLU* 1.3 71.1 + - - +
55F LEU* 4.2 6.5 - - + -
175F THR* 3.6 25.1 - - + -
179F LEU* 3.7 29.8 - - + -
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Residues in contact with GLU 54 (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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4F ILE 2.6 13.0 + - - +
5F ARG* 3.4 31.7 - - + +
6F LYS 3.1 23.7 + - - +
43F VAL* 3.7 30.7 - - + +
44F ALA 3.7 2.7 - - - -
45F ASP* 4.1 14.2 + - - +
52F GLN 4.3 0.4 + - - -
53F VAL* 1.3 72.0 - - - +
55F LEU* 1.3 61.6 + - - +
56F ALA* 3.7 2.9 + - + +
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Residues in contact with LEU 55 (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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6F LYS* 3.6 31.9 - - + +
7F LYS 4.9 0.4 - - - -
8F LEU* 4.3 28.5 - - + -
43F VAL* 3.4 5.5 - - - -
44F ALA* 2.7 47.7 + - + +
46F ILE* 4.2 9.4 - - + -
53F VAL* 3.6 9.2 + - + -
54F GLU* 1.3 70.6 - - - +
56F ALA* 1.3 63.7 + - - +
57F LEU* 3.5 15.1 + - + +
79F VAL* 5.0 5.8 - - + -
171F PHE* 4.5 16.8 - - + +
175F THR* 3.5 29.6 - - - +
178F ALA* 5.2 0.2 - - + -
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Residues in contact with ALA 56 (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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6F LYS 2.9 13.6 + - - +
7F LYS* 4.4 4.9 - - + -
8F LEU* 2.8 34.3 + - - +
41F ASN* 5.9 0.9 - - - +
42F TYR 3.6 7.4 - - - +
43F VAL* 4.6 8.1 - - + -
54F GLU* 3.7 5.0 + - - +
55F LEU* 1.3 70.3 - - - +
57F LEU* 1.3 58.6 + - - +
58F TRP* 3.7 19.4 - - - +
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Residues in contact with LEU 57 (chain F).
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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8F LEU* 3.7 27.8 - - + -
22F LEU* 4.1 37.5 - - + +
25F ASN* 5.1 2.2 - - - +
41F ASN* 3.3 6.4 - - - +
42F TYR* 2.7 60.5 + - + +
43F VAL 4.5 1.3 - - - +
44F ALA* 4.1 20.2 - - + +
55F LEU* 3.8 21.8 - - + +
56F ALA* 1.3 74.1 - - - +
58F TRP* 1.3 62.8 + - - +
59F ASP 3.7 1.5 + - - -
171F PHE* 4.1 19.3 - - + -
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Residues in contact with TRP 58 (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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7F LYS* 3.4 46.9 - - + +
8F LEU* 2.8 23.4 + - - +
9F VAL* 3.6 15.0 - - + +
10F ILE* 3.1 27.4 + - - +
39F PHE* 3.7 32.1 - + - -
40F GLU 4.0 4.3 - - - -
41F ASN* 3.4 21.8 - - - +
56F ALA* 3.7 20.7 - - - +
57F LEU* 1.3 73.0 - - - +
59F ASP* 1.3 60.7 + - - +
60F THR* 4.7 0.7 - - - -
72F LEU 4.2 5.8 - - - -
73F SER* 3.8 25.8 - - - +
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Residues in contact with ASP 59 (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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10F ILE* 3.7 13.4 - - - +
18F LYS* 4.1 7.4 - - - +
19F THR* 2.5 39.9 + - - +
22F LEU* 3.6 19.5 - - + +
37F THR* 3.6 14.9 + - + +
39F PHE* 4.0 6.4 - - - -
40F GLU* 2.9 35.2 + - + +
42F TYR* 3.9 12.5 + - + -
57F LEU 3.7 1.2 + - - -
58F TRP* 1.3 72.8 - - - +
60F THR* 1.3 76.0 + - - +
73F SER* 4.6 4.0 + - - -
202F MG 4.2 0.2 - - - -
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Residues in contact with THR 60 (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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9F VAL* 4.0 10.3 - - + -
10F ILE 2.7 27.0 + - - +
11F VAL* 3.8 12.0 - - + +
12F GLY 5.0 0.3 + - - -
18F LYS* 3.6 17.3 - - - -
37F THR* 4.0 11.4 - - - -
38F VAL 4.3 6.3 - - - -
39F PHE* 6.1 0.4 - - + -
58F TRP 4.1 1.1 - - - +
59F ASP* 1.3 87.5 + - - +
61F ALA* 1.3 62.9 + - - +
70F ARG* 4.0 26.2 - - + -
73F SER* 3.8 27.8 - - - +
203F MGF 4.0 1.0 - - - -
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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