Contacts of the strand formed by residues 91 - 98 (chain F) in PDB entry 1LE9
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 ALA 91 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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84F ILE* 4.0 18.2 - - + -
88F VAL* 3.4 20.4 - - + -
89F GLY 5.0 0.9 - - - +
90F PRO* 1.3 79.0 - - - +
92F LYS* 1.3 57.4 + - - +
93F VAL* 5.5 1.6 - - + -
124F THR* 3.4 6.7 - - - +
125F ALA* 2.7 44.9 + - + -
216F ALA* 5.6 0.2 - - + -
217F PHE 3.6 9.9 - - - +
218F LEU* 4.1 2.7 - - + -
225F PHE* 3.6 11.8 - - - -
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Residues in contact with LYS 92 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91F ALA* 1.3 72.7 - - - +
93F VAL* 1.3 57.7 + - - +
94F ILE* 2.9 32.2 - - + +
122F THR* 3.4 21.8 - - + -
123F VAL 3.6 6.1 - - - +
124F THR* 4.7 5.6 - - + +
163F TYR* 3.8 19.5 - - - +
216F ALA* 3.5 0.2 - - - -
217F PHE* 2.7 71.2 + - - +
225F PHE* 3.6 37.9 - - + -
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Residues in contact with VAL 93 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42F LEU* 3.2 30.1 - - + -
82F VAL* 4.7 8.1 - - + -
84F ILE* 5.0 7.4 - - + -
91F ALA 4.1 0.4 + - - -
92F LYS* 1.3 71.9 - - - +
94F ILE* 1.3 67.2 + - - +
121F CYS 3.8 2.8 - - - +
123F VAL* 3.0 42.1 + - + +
125F ALA* 4.9 12.6 - - + -
134F PHE* 3.9 10.7 - - + -
214F PHE* 4.2 14.4 - - + -
215F THR 3.2 3.6 - - - +
216F ALA* 3.3 27.1 - - + -
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Residues in contact with ILE 94 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92F LYS* 2.9 53.2 - - + +
93F VAL* 1.3 74.0 - - - +
95F VAL* 1.3 66.2 + - - +
96F GLN* 4.9 1.8 - - + +
120F VAL* 4.0 30.1 - - + +
121F CYS 3.6 3.8 - - - -
122F THR* 3.5 18.6 - - + +
163F TYR* 4.3 36.1 - - + -
213F MET* 3.4 6.1 - - + +
214F PHE* 4.0 0.3 - - - -
215F THR* 2.8 40.6 + - - +
217F PHE* 4.4 3.4 - - + -
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Residues in contact with VAL 95 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94F ILE* 1.3 79.2 - - - +
96F GLN* 1.3 63.5 + - - +
111F LEU* 3.3 17.8 - - + +
120F VAL* 3.3 19.9 - - - -
121F CYS* 3.1 21.7 + - + +
134F PHE* 3.1 38.8 - - + -
137F LEU* 5.1 1.8 - - + -
212F LEU* 4.2 15.9 - - + -
213F MET 3.5 25.4 - - - +
214F PHE* 4.3 12.3 - - + +
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Residues in contact with GLN 96 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94F ILE* 5.4 1.7 - - + +
95F VAL* 1.3 75.8 - - - +
97F LEU* 1.3 77.9 + - + +
106F LEU* 3.3 29.0 - - - +
111F LEU* 3.6 9.2 - - - -
119F GLY 3.6 14.1 - - - +
120F VAL* 4.1 13.0 - - + +
154F ARG* 3.3 24.0 - - - +
158F ALA* 5.1 6.7 - - - +
163F TYR* 4.9 4.6 + - - +
164F ASN* 4.6 7.7 - - - +
168F LEU* 3.8 11.6 - - - +
212F LEU* 3.6 1.4 - - - -
213F MET* 2.9 61.5 + - + +
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Residues in contact with LEU 97 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96F GLN* 1.3 85.7 - - + +
98F VAL* 1.3 61.5 + - - +
106F LEU* 3.9 1.9 - - - -
107F HIS* 3.0 22.3 + - + +
109F HIS* 3.2 41.3 - - + +
110F SER* 3.5 5.2 - - - +
111F LEU* 3.0 53.8 - - + +
119F GLY 3.8 8.5 - - - +
139F ILE* 4.2 15.0 - - + -
154F ARG* 4.3 7.2 - - - +
210F VAL* 3.4 20.2 - - + -
211F ARG 3.6 6.1 - - - -
212F LEU* 5.1 1.8 - - + +
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Residues in contact with VAL 98 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97F LEU* 1.3 73.9 - - - +
99F THR* 1.3 60.9 + - - +
104F ILE* 4.1 9.0 - - + -
105F HIS 3.0 9.6 - - - +
107F HIS* 3.3 4.4 - - - +
168F LEU* 3.0 35.7 - - + -
210F VAL* 3.1 23.7 - - - +
211F ARG* 2.8 53.5 + - + +
212F LEU 3.9 6.5 - - - +
213F MET* 3.3 26.5 - - + -
233F VAL* 4.2 12.3 - - + -
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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