Contacts of the strand formed by residues 14 - 19 (chain H) in PDB entry 5FUR
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 SER 14 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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641G LEU* 3.3 30.1 - - - +
644G TYR* 4.4 2.9 + - - -
786G ILE* 3.6 1.4 - - - +
787G ARG* 2.8 65.9 + - - +
12H LEU 3.5 4.6 + - - -
13H GLU* 1.3 73.6 - - - +
15H GLN* 1.3 64.7 + - - +
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Residues in contact with GLN 15 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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641G LEU* 5.6 0.5 - - - +
694G GLY* 3.8 9.7 - - - -
784G LEU* 3.8 11.5 - - + +
785G ILE 3.3 6.7 - - - +
786G ILE* 4.1 17.6 - - + +
13H GLU* 3.1 26.5 + - - +
14H SER* 1.3 81.2 + - - +
16H PHE* 1.3 68.0 + - - +
76H SER* 2.6 28.3 + - - -
88H THR* 3.0 22.0 + - - -
89H ALA* 3.4 18.0 - - + +
90H ASP 4.2 4.6 + - - +
91H ILE* 3.8 32.5 - - + +
92H CYS 4.9 1.2 + - - -
93H GLN 5.4 0.2 + - - -
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Residues in contact with PHE 16 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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641G LEU* 4.0 27.1 - - + -
784G LEU* 3.8 3.8 - - - +
785G ILE* 2.8 71.6 + - + +
787G ARG* 4.1 25.4 - - + -
792G TYR* 4.1 11.9 - + - -
15H GLN* 1.3 80.4 - - - +
17H ILE* 1.3 76.4 + - - +
18H LEU* 5.1 0.4 - - + -
45H ILE* 4.4 6.7 - - + -
47H LEU* 5.8 1.6 - - + -
67H LEU* 4.8 7.2 - - + -
91H ILE* 4.1 5.6 - - - -
93H GLN* 3.4 23.8 - - + +
95H LEU* 3.9 30.5 - - + -
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Residues in contact with ILE 17 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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701G LEU* 4.2 15.3 - - + -
778G MET* 4.0 19.3 - - + -
782G ASP* 3.9 26.2 - - + +
783G PHE 3.5 12.3 - - - +
784G LEU* 4.4 10.8 - - + -
16H PHE* 1.3 83.7 - - - +
18H LEU* 1.3 66.8 + - - +
70H LEU* 4.6 10.5 - - + -
74H MET* 4.6 6.1 - - - -
91H ILE* 4.1 20.4 - - + -
93H GLN 3.2 6.3 + - - +
94H MET* 3.2 20.8 - - + +
95H LEU 2.7 32.6 + - - -
136H ILE* 4.9 3.6 - - + -
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Residues in contact with LEU 18 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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781G THR 3.5 1.9 - - - +
782G ASP* 3.3 4.9 - - - -
783G PHE* 2.9 42.6 + - + +
785G ILE* 3.6 32.5 - - + -
794G ILE* 4.6 1.3 - - + -
16H PHE* 3.9 2.0 + - + -
17H ILE* 1.3 73.9 - - - +
19H ARG* 1.3 59.7 + - - +
20H LEU* 4.0 38.1 - - + -
43H LEU* 4.3 21.1 - - + -
45H ILE* 5.0 5.6 - - + -
56H VAL* 4.1 21.8 - - + -
95H LEU* 3.6 25.4 - - + +
97H SER* 4.1 2.0 - - - +
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Residues in contact with ARG 19 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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779G PRO* 4.0 13.5 - - - +
781G THR* 3.5 17.3 + - + +
782G ASP* 2.8 39.5 + - - +
17H ILE 4.0 0.4 + - - -
18H LEU* 1.3 73.9 - - - +
20H LEU* 1.3 65.5 + - - +
94H MET* 3.7 28.2 - - + +
95H LEU 2.9 13.3 + - - +
96H VAL* 4.4 15.9 - - + -
97H SER* 3.0 32.7 + - - +
132H TRP* 3.9 27.0 - - - +
136H ILE* 3.8 19.6 + - - +
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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