Contacts of the strand formed by residues 96 - 103 (chain E) in PDB entry 4FMB
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 ILE 96 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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91E CYS 4.0 0.2 - - - +
92E LEU* 3.5 2.8 - - - +
93E ASN* 2.9 31.4 + - - +
94E LYS* 3.5 19.5 - - + +
95E GLY* 1.3 82.8 - - - +
97E CYS* 1.3 63.8 + - - +
98E SER* 3.8 6.1 + - - -
111E GLN* 3.6 43.7 - - + +
112E LEU 4.1 11.0 - - - +
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Residues in contact with CYS 97 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78E PHE* 4.3 9.4 - - - -
90E LEU* 4.8 3.8 - - - -
91E CYS 3.2 14.8 - - - +
92E LEU* 4.3 4.8 - - + +
95E GLY 4.2 1.2 + - - -
96E ILE* 1.3 74.8 - - - +
98E SER* 1.3 61.5 + - - +
111E GLN* 3.8 0.7 - - - -
112E LEU* 2.8 43.4 + - + +
117E TYR* 3.1 49.2 - - + +
120E LEU* 3.9 19.7 - - - -
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Residues in contact with SER 98 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89E ARG 3.6 1.6 - - - +
90E LEU* 3.9 2.1 - - - -
91E CYS* 3.0 29.1 + - - +
93E ASN* 4.0 17.0 + - - -
96E ILE 4.1 3.1 + - - -
97E CYS* 1.3 76.3 - - - +
99E VAL* 1.3 65.0 + - - +
100E PHE* 3.8 23.1 - - - -
109E SER* 5.3 1.6 - - - -
110E THR 3.0 15.3 - - - -
111E GLN* 3.9 14.1 - - - +
112E LEU 4.3 0.2 - - - +
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Residues in contact with VAL 99 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88E ILE* 3.3 29.2 - - + -
89E ARG 3.6 1.8 - - - -
90E LEU* 3.7 20.9 - - + -
97E CYS* 5.1 0.2 - - - -
98E SER* 1.3 75.6 - - - +
100E PHE* 1.3 64.8 + - - +
101E TYR* 3.5 32.7 - - + +
109E SER* 3.0 5.4 - - - -
110E THR* 2.6 41.1 + - - +
112E LEU* 4.0 29.2 - - + -
120E LEU* 4.9 0.7 - - + -
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Residues in contact with PHE 100 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74E MET* 3.9 26.7 - - + -
87E SER 3.5 1.2 - - - +
88E ILE* 3.1 8.1 - - - +
89E ARG* 2.8 44.3 + - + +
91E CYS* 4.0 21.3 - - + -
93E ASN* 5.5 2.7 - - - -
98E SER* 3.8 28.9 - - - -
99E VAL* 1.3 78.5 - - - +
101E TYR* 1.3 60.9 + - - +
102E LEU* 3.8 12.6 - - + -
107E ILE* 4.2 16.4 - - + -
108E GLN 3.4 2.7 - - - -
109E SER* 3.6 26.5 - - - -
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Residues in contact with TYR 101 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48E PRO* 4.1 35.4 - - + +
49E HIS* 3.5 48.9 + + + -
52E LEU* 4.4 8.3 - - + -
86E ILE* 4.5 2.9 - - + -
87E SER 3.8 3.4 - - - -
88E ILE* 3.8 26.9 - - + -
99E VAL* 3.5 34.4 - - + +
100E PHE* 1.3 72.6 - - - +
102E LEU* 1.3 63.1 + - - +
103E ASP* 3.9 1.5 + - - +
106E LYS 3.9 1.2 - - - +
107E ILE* 3.7 3.8 - - - -
108E GLN* 2.8 49.0 + - + +
109E SER* 5.0 0.4 - - - -
110E THR* 4.5 13.4 + - - -
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Residues in contact with LEU 102 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74E MET* 4.7 11.7 - - + -
85E GLY 4.1 1.2 - - - +
86E ILE* 3.7 4.1 - - - +
87E SER* 3.0 43.2 + - - +
89E ARG* 3.6 41.1 - - + +
100E PHE* 3.8 25.1 - - + -
101E TYR* 1.3 79.0 - - - +
103E ASP* 1.3 60.4 + - - +
104E GLY 3.8 6.2 + - - +
106E LYS 3.7 6.5 - - - +
107E ILE* 4.5 20.2 - - + -
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Residues in contact with ASP 103 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46E TYR* 3.4 30.5 + - - -
48E PRO* 4.0 15.9 - - + +
84E ASP 5.5 0.2 - - - +
85E GLY 4.1 11.2 - - - +
86E ILE* 4.4 15.4 - - + +
101E TYR 3.9 1.3 - - - +
102E LEU* 1.3 71.8 - - - +
104E GLY* 1.3 61.5 + - - +
105E ASP 2.8 10.7 + - - -
106E LYS* 3.2 25.5 + - + +
108E GLN* 5.5 2.7 - - - +
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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