Contacts of the strand formed by residues 57 - 61 (chain A) in PDB entry 4FUF
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 TYR 57 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A ILE* 4.0 14.6 - - + -
19A TYR 3.4 14.1 - - - +
20A ARG* 3.9 23.6 - - + -
21A ARG* 3.3 14.0 + - - -
30A VAL* 4.2 9.0 - - + -
47A CYS 4.2 1.9 + - - -
48A PHE* 3.5 41.2 - + - -
51A TYR* 2.6 41.1 + - - +
53A LYS 3.3 20.6 - - - -
54A LYS* 3.2 13.0 + - - +
55A GLU 4.1 1.0 - - - +
56A ASP* 1.3 82.0 - - + +
58A ILE* 1.3 61.3 - - - +
59A VAL 4.3 0.2 - - - -
77A GLU* 4.1 14.9 - - - +
78A VAL* 3.7 23.7 + - + -
81A LEU* 4.2 10.3 - - + -
101A LEU* 5.3 0.7 - - + -
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Residues in contact with ILE 58 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A ALA 3.7 1.2 - - - +
18A ILE* 3.5 3.6 - - - +
19A TYR* 2.8 40.1 + - + +
21A ARG* 3.5 51.6 - - + +
27A VAL* 3.8 31.2 - - + -
57A TYR* 1.3 72.5 - - - +
59A VAL* 1.4 65.4 + - - +
60A TYR* 3.6 25.8 - - + -
75A LYS* 3.8 30.3 - - + +
76A PHE 3.6 4.9 - - - +
307A GOL 4.0 6.5 - - - +
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Residues in contact with VAL 59 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16A ALA* 4.1 24.9 - - + -
17A ALA 3.6 4.5 - - - +
18A ILE* 4.4 10.8 - - + -
41A VAL* 4.2 7.4 - - + -
58A ILE* 1.4 78.4 - - - +
60A TYR* 1.3 65.9 + - - +
61A LEU* 5.1 2.2 - - + -
75A LYS* 3.6 2.1 - - - +
76A PHE* 2.7 48.6 + - + +
78A VAL* 3.8 26.5 - - + -
101A LEU* 4.0 14.8 - - + -
103A ILE* 4.0 26.7 - - + -
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Residues in contact with TYR 60 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15A PHE 4.2 0.7 - - - +
16A ALA* 3.5 7.8 - - - +
17A ALA* 2.9 35.5 + - + +
19A TYR* 3.5 23.8 - + - -
58A ILE* 3.6 12.8 - - + -
59A VAL* 1.3 76.8 - - - +
61A LEU* 1.3 61.9 + - - +
63A ARG* 3.3 46.2 + - + +
69A ASN* 4.6 3.0 + - - -
73A GLU* 3.4 20.9 - - + -
74A MET 3.3 12.3 - - - -
75A LYS* 3.7 37.7 + - + +
307A GOL 2.7 43.2 + - - -
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Residues in contact with LEU 61 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13A PRO 5.2 1.8 - - - +
14A TRP 4.6 1.6 - - - +
15A PHE 4.1 7.6 - - - +
16A ALA* 3.8 30.5 - - + -
35A LEU* 3.8 32.3 - - + -
41A VAL* 4.6 2.7 - - + -
59A VAL* 5.1 1.8 - - + -
60A TYR* 1.3 72.9 - - - +
62A GLY* 1.3 64.3 + - - +
63A ARG* 3.2 2.9 + - - +
73A GLU* 3.2 2.9 - - - +
74A MET 2.9 28.6 + - - -
76A PHE* 3.6 20.9 - - + -
103A ILE* 3.9 4.5 - - + -
111A ALA* 3.4 33.2 - - + -
117A ILE* 3.8 26.0 - - + -
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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