Contacts of the strand formed by residues 96 - 104 (chain A) in PDB entry 5FDK
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 ARG 96 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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92A ILE* 3.4 7.6 - - - -
93A TYR 2.8 34.6 + - - +
94A LYS 2.7 10.6 + - - +
95A GLY* 1.3 73.9 - - - -
97A TYR* 1.3 67.4 + - - +
98A ILE* 4.3 0.4 - - - +
131A ASP 6.1 0.2 - - - +
132A GLY* 6.4 0.4 - - - -
133A ILE* 4.5 10.8 - - + -
198A PHE* 4.3 16.2 - - + -
95C GLY 3.9 10.8 - - - +
97C TYR* 4.1 3.0 - - - +
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Residues in contact with TYR 97 (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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86A THR* 5.2 1.0 - - - +
90A ASN* 3.5 15.9 + - + -
91A GLY 3.5 3.1 - - - -
96A ARG* 1.3 73.6 - - - +
98A ILE* 1.3 73.0 + - - +
99A ASP* 2.8 37.9 + - + -
123A HIS* 4.6 6.8 + - - -
127A VAL* 3.7 23.3 - - + +
132A GLY* 4.1 8.5 - - - -
133A ILE* 3.1 25.3 + - - +
53C VAL* 5.2 3.4 - - + +
91C GLY* 2.9 48.8 - - - -
92C ILE* 3.5 28.3 - - + -
95C GLY 4.0 6.6 + - - +
97C TYR* 3.7 23.8 - + - +
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Residues in contact with ILE 98 (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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52A ALA* 6.1 0.7 - - + -
54A ILE* 5.5 5.8 - - + -
90A ASN* 3.2 8.1 - - - +
91A GLY* 2.9 38.2 + - - +
92A ILE 4.4 2.0 - - - -
93A TYR* 4.1 33.4 - - + +
96A ARG 4.4 2.7 - - - +
97A TYR* 1.3 90.2 - - - +
99A ASP* 1.3 65.4 + - - +
100A PHE* 3.7 27.8 - - + -
133A ILE* 3.6 33.7 - - + -
135A PHE* 4.0 10.5 - - + -
189A TYR* 5.2 3.6 - - + -
193A ILE* 4.7 12.6 - - + -
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Residues in contact with ASP 99 (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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86A THR* 4.4 3.4 - - - +
87A THR* 2.9 34.2 - - - -
89A TYR 3.3 9.9 - - - -
90A ASN* 3.4 8.1 + - - +
97A TYR* 2.8 38.0 + - + -
98A ILE* 1.3 74.4 - - - +
100A PHE* 1.3 68.2 + - - +
123A HIS* 3.7 18.7 + - - -
127A VAL* 3.9 14.4 - - + -
133A ILE 3.0 13.1 + - - +
134A CYS* 3.1 7.7 - - + -
135A PHE* 3.0 18.6 + - - -
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Residues in contact with PHE 100 (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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39A LEU* 4.3 8.7 - - + -
43A ASN* 4.8 1.3 - - - -
54A ILE* 5.1 5.6 - - + -
87A THR* 3.8 6.2 - - - -
88A ASN 3.8 2.9 + - - -
89A TYR* 2.9 76.2 + + + +
98A ILE* 3.7 16.6 - - + -
99A ASP* 1.3 81.9 + - - +
101A GLU* 1.3 67.7 + - - +
102A ALA* 4.8 0.4 - - + -
124A MET* 5.5 0.4 - - - -
134A CYS* 5.5 0.9 - - - -
135A PHE* 3.0 50.5 - + + +
137A ILE* 3.4 30.1 - - + -
189A TYR* 4.1 24.5 - + - -
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Residues in contact with GLU 101 (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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87A THR* 4.5 2.6 - - - -
88A ASN* 3.8 10.8 - - + +
100A PHE* 1.3 81.8 - - - +
102A ALA* 1.3 60.1 + - - +
103A LYS* 3.8 16.6 - - + +
116A PHE* 3.7 31.2 - - + -
120A GLN* 5.7 1.1 - - + +
124A MET* 3.8 13.3 - - + +
135A PHE 3.0 7.7 + - - +
136A VAL* 3.5 3.4 - - + -
137A ILE 2.9 24.1 + - - -
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Residues in contact with ALA 102 (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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39A LEU* 3.7 30.1 - - + -
88A ASN* 4.0 12.0 + - + +
89A TYR* 4.4 13.0 - - + -
100A PHE* 4.5 1.1 - - + -
101A GLU* 1.3 74.5 - - - +
103A LYS* 1.3 74.3 + - - +
137A ILE* 3.2 12.3 - - + +
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Residues in contact with LYS 103 (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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88A ASN* 2.5 30.8 + - - +
101A GLU* 3.8 10.3 - - + +
102A ALA* 1.3 81.2 - - - +
104A GLU* 1.3 61.4 + - - +
111A PHE* 3.4 25.6 - - + -
115A ASN* 3.6 32.5 - - - +
116A PHE* 3.9 24.8 - - + -
120A GLN* 3.0 28.2 - - - +
136A VAL* 5.0 0.6 - - + +
137A ILE 2.9 7.4 + - - +
138A ILE* 3.1 11.6 - - - +
139A SER 2.9 19.9 + - - -
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Residues in contact with GLU 104 (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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30A ASN* 4.3 7.7 - - - +
31A ARG 3.3 4.9 + - - +
32A GLY* 2.4 39.3 + - - +
33A MET* 2.6 38.2 + - - +
35A LEU* 4.8 0.2 - - - +
103A LYS* 1.3 75.9 - - - +
105A THR* 1.3 63.3 + - - +
111A PHE* 4.2 2.9 - - - -
115A ASN* 4.4 8.0 + - - +
139A SER* 3.1 25.8 - - - +
3E G 4.4 18.4 + - - +
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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