Contacts of the strand formed by residues 133 - 140 (chain B) 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 ILE 133 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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93B TYR* 6.1 0.4 - - + -
96B ARG* 4.2 19.7 - - + -
97B TYR 2.9 18.2 + - - +
98B ILE* 3.4 24.1 - - + +
99B ASP* 2.9 27.8 + - - +
127B VAL* 5.1 0.2 - - - -
128B LYS* 5.4 0.7 - - - +
131B ASP* 5.4 2.7 - - - +
132B GLY* 1.3 71.1 - - - +
134B CYS* 1.3 61.9 + - - +
135B PHE* 3.6 25.2 - - + -
146B PHE* 5.7 0.9 - - + -
193B ILE* 3.9 25.4 - - + -
197B TYR* 4.7 11.0 - - + -
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Residues in contact with CYS 134 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87B THR* 5.5 0.2 - - - -
99B ASP* 4.0 16.4 - - - -
124B MET* 3.7 39.9 - - - -
127B VAL* 3.8 20.4 - - + -
128B LYS* 3.9 14.7 - - + +
132B GLY 3.6 2.2 + - - +
133B ILE* 1.3 75.7 - - - +
135B PHE* 1.3 70.8 + - - +
148B GLU* 4.3 9.4 - - - +
149B ALA* 3.3 30.2 + - + +
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Residues in contact with PHE 135 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98B ILE* 3.6 14.1 - - + -
99B ASP 3.5 2.4 + - - +
100B PHE* 3.5 21.7 - - + -
101B GLU* 3.3 21.5 + - - +
133B ILE* 3.6 15.0 - - + -
134B CYS* 1.3 85.3 - - - +
136B VAL* 1.3 60.5 + - - +
137B ILE* 3.5 37.7 - - + -
146B PHE* 3.3 38.6 - + + -
147B LEU 3.3 17.3 - - - +
148B GLU* 4.4 1.1 - - - +
149B ALA* 4.2 6.3 - - - +
152B LEU* 6.2 0.4 - - - -
189B TYR* 4.2 10.1 - + - -
193B ILE* 3.5 33.9 - - + -
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Residues in contact with VAL 136 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101B GLU* 3.3 34.8 - - + +
102B ALA 4.3 0.9 - - - +
103B LYS* 4.3 4.5 - - + -
116B PHE* 3.6 22.0 - - + -
135B PHE* 1.3 74.1 - - - +
137B ILE* 1.3 69.7 + - - +
138B ILE* 3.8 12.0 + - + -
147B LEU* 2.9 61.2 + - + +
148B GLU 5.1 0.2 - - - -
149B ALA* 5.3 1.0 - - - +
152B LEU* 4.2 19.2 - - + +
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Residues in contact with ILE 137 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35B LEU* 4.2 14.1 - - + +
39B LEU* 4.6 13.2 - - + -
100B PHE* 4.6 8.5 - - + -
101B GLU 2.5 18.6 + - - +
102B ALA* 3.4 3.7 - - - -
103B LYS 3.0 27.2 + - - +
135B PHE* 3.5 34.5 - - + -
136B VAL* 1.3 71.3 - - - +
138B ILE* 1.3 65.8 + - - +
144B VAL* 5.3 5.8 - - + -
145B TYR 3.6 11.4 - - - +
146B PHE* 4.8 5.2 - - + -
179B ILE* 5.6 2.5 - - + -
187B ILE* 5.0 13.2 - - + -
189B TYR* 3.7 36.1 - - + -
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Residues in contact with ILE 138 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103B LYS* 3.4 5.2 - - + +
111B PHE* 3.7 53.6 - - + -
136B VAL* 4.0 17.0 - - + +
137B ILE* 1.3 79.2 - - - +
139B SER* 1.3 70.8 + - - +
140B ALA* 3.7 5.8 + - + +
144B VAL* 3.3 2.5 - - - -
145B TYR* 2.8 44.3 + - + +
147B LEU* 3.7 34.3 - - + -
172B LEU* 4.2 22.4 - - + -
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Residues in contact with SER 139 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34B THR* 5.6 2.3 - - - +
35B LEU* 3.8 21.0 - - - +
103B LYS 2.9 13.1 + - - -
104B GLU* 3.5 16.1 - - - +
105B THR 3.2 21.3 + - - +
137B ILE 4.1 0.2 + - - -
138B ILE* 1.3 73.9 - - - +
140B ALA* 1.3 64.3 + - - +
143B GLN 3.4 5.7 + - - -
144B VAL* 3.7 21.2 - - - +
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Residues in contact with ALA 140 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105B THR* 3.4 37.2 - - + +
111B PHE* 5.2 0.4 - - + -
138B ILE* 3.7 12.6 + - + +
139B SER* 1.3 76.7 - - - +
141B PHE* 1.3 81.7 + - + +
142B ASP 3.1 2.9 - - - +
143B GLN* 2.6 33.3 + - - +
145B TYR* 3.4 6.9 - - + -
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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