Contacts of the strand formed by residues 104 - 109 (chain A) in PDB entry 5FFO
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 104 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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100A SER* 2.8 25.3 + - - -
101A LYS* 2.9 41.1 + - + +
102A GLN* 4.7 9.2 - - - -
103A ASP* 1.3 85.2 - - - +
105A ILE* 1.3 57.3 + - - +
106A LEU 4.2 0.2 - - - -
130A LEU* 4.4 17.3 - - + +
131A GLN 3.6 4.5 - - - +
132A ASP* 3.2 36.8 + - + +
163A PHE* 4.6 14.6 - - + -
167A ASP* 4.1 21.1 + - - -
188A VAL* 4.4 23.6 - - + +
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Residues in contact with ILE 105 (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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26A PHE* 3.7 35.4 - - + -
37A LEU* 3.6 45.8 - - + -
56A VAL* 5.1 0.9 - - + -
58A LYS* 6.3 0.2 - - + -
70A ILE* 4.2 13.2 - - + -
72A PHE* 3.9 24.8 - - + -
98A VAL* 4.4 11.0 - - + -
99A ARG 4.0 2.2 - - - +
100A SER* 3.9 0.9 - - - +
103A ASP 4.9 0.4 - - - +
104A LYS* 1.3 78.8 - - - +
106A LEU* 1.3 62.2 + - - +
107A ALA 4.2 0.2 + - - -
129A PHE 3.9 1.6 - - - +
130A LEU* 3.4 4.7 - - - +
131A GLN* 3.1 41.2 + - + +
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Residues in contact with LEU 106 (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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98A VAL* 3.5 3.6 - - - +
99A ARG 2.9 39.7 + - - +
104A LYS 4.2 0.2 - - - -
105A ILE* 1.3 75.8 - - - +
107A ALA* 1.3 62.3 + - - +
108A CYS* 4.5 1.8 - - - -
128A CYS* 4.1 19.5 - - + -
129A PHE 3.9 9.9 - - - +
130A LEU* 4.2 18.6 - - + -
139A TYR* 5.3 7.4 - - + -
161A ILE* 3.5 33.6 - - + +
162A ASP 5.3 1.3 - - - +
163A PHE* 3.7 24.7 - - + -
169A VAL* 3.8 31.2 - - + -
171A LEU* 6.5 0.2 - - + -
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Residues in contact with ALA 107 (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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56A VAL* 3.6 22.7 - - + -
72A PHE* 4.2 10.1 - - + -
94A PHE* 3.5 28.1 - - + -
95A GLY* 4.8 0.9 - - - -
97A SER 3.7 7.6 - - - +
98A VAL* 4.7 3.8 - - + -
105A ILE 4.1 0.8 - - - -
106A LEU* 1.3 74.3 - - - +
108A CYS* 1.3 64.8 + - - +
128A CYS* 3.3 3.8 - - - +
129A PHE 2.9 33.3 + - - +
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Residues in contact with CYS 108 (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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94A PHE* 3.4 5.3 - - - -
95A GLY 2.9 21.8 + - - -
96A ALA 3.7 3.1 + - - -
97A SER* 3.6 10.1 + - - +
106A LEU* 4.5 2.5 - - - -
107A ALA* 1.3 77.3 - - - +
109A ALA* 1.3 60.7 + - - +
110A PRO* 3.4 7.2 - - - +
127A THR 3.5 4.5 - - - -
128A CYS* 2.0 45.5 - - - -
158A GLY* 3.3 31.2 - - - +
161A ILE* 3.8 24.5 - - - -
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Residues in contact with ALA 109 (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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92A GLN* 3.3 43.1 - - + +
93A TRP 3.7 1.8 - - - -
94A PHE* 3.7 11.9 - - + -
108A CYS* 1.3 72.6 - - - +
110A PRO* 1.3 66.7 - - - +
111A LEU 3.2 2.5 - - - -
112A TYR* 3.2 17.9 + - + +
126A GLY* 3.5 10.0 - - - -
127A THR* 2.8 19.2 + - + +
129A PHE* 6.1 0.2 - - + -
157A GLY 4.7 1.1 - - - -
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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