Contacts of the strand formed by residues 92 - 98 (chain B) in PDB entry 1LEI
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 92 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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91B ALA* 1.3 76.5 - - - +
93B VAL* 1.3 62.9 + - - +
94B ILE* 4.0 13.4 + - + -
122B THR* 3.7 24.7 - - + -
123B VAL 3.7 12.8 - - - +
124B THR* 5.8 0.7 - - + -
161B ARG* 4.9 5.3 - - - +
163B TYR* 4.0 26.8 - - - +
215B THR 4.0 0.3 - - - +
216B ALA* 3.4 1.9 - - - +
217B PHE* 2.7 51.7 + - + +
225B PHE* 3.7 43.1 + - + +
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Residues in contact with VAL 93 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B LEU* 4.7 10.3 - - + -
82B VAL* 4.9 11.0 - - + -
84B ILE* 3.7 22.2 - - + -
92B LYS* 1.3 78.8 - - - +
94B ILE* 1.3 72.7 + - - +
121B CYS 4.5 0.2 - - - +
123B VAL* 2.9 48.0 + - + +
124B THR* 5.1 0.6 - - - +
125B ALA* 5.0 1.1 - - + -
132B VAL* 4.8 13.9 - - + -
134B PHE* 4.4 15.7 - - + -
214B PHE* 5.3 0.9 - - + -
215B THR 3.3 13.5 - - - +
216B ALA* 3.7 18.2 - - + -
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Residues in contact with ILE 94 (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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92B LYS* 4.0 24.0 - - - -
93B VAL* 1.3 84.8 - - - +
95B VAL* 1.3 69.7 + - - +
96B GLN* 4.7 6.7 - - - +
120B VAL* 4.4 5.8 - - + -
121B CYS 3.3 11.2 - - - +
122B THR* 3.8 17.9 - - + +
134B PHE* 5.2 0.7 - - - -
163B TYR* 2.8 51.4 - - + +
164B ASN* 4.3 5.2 - - - +
213B MET 5.4 0.4 - - - +
214B PHE* 3.7 2.9 - - - -
215B THR* 2.8 44.5 + - - +
217B PHE* 3.6 10.3 - - + -
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Residues in contact with VAL 95 (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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94B ILE* 1.3 82.2 - - - +
96B GLN* 1.3 64.8 + - - +
111B LEU* 3.5 20.5 - - + +
120B VAL* 2.9 21.5 - - - +
121B CYS* 3.0 35.6 + - + +
134B PHE* 3.8 17.9 - - + -
137B LEU* 5.3 0.7 - - + -
212B LEU* 4.1 15.7 - - + -
213B MET 3.4 12.6 - - - +
214B PHE* 3.7 29.2 - - + -
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Residues in contact with GLN 96 (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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94B ILE* 4.7 6.2 - - + +
95B VAL* 1.3 77.8 - - - +
97B LEU* 1.3 67.2 + - - +
98B VAL* 4.5 0.2 - - + -
106B LEU* 3.1 23.1 - - + +
111B LEU* 4.7 1.1 - - - -
119B GLY 4.8 1.8 - - - +
120B VAL* 4.1 18.1 - - + +
158B ALA* 5.3 0.2 - - - +
163B TYR 4.4 2.4 + - - -
164B ASN* 3.5 26.2 + - - +
165B PRO* 3.1 32.9 - - - +
168B LEU* 3.4 15.9 - - + +
213B MET* 3.1 45.8 + - + +
215B THR* 5.1 2.4 + - - -
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Residues in contact with LEU 97 (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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96B GLN* 1.3 75.2 - - - +
98B VAL* 1.3 64.5 - - - +
106B LEU* 4.2 7.3 - - - +
107B HIS* 3.5 21.7 + - + +
109B HIS* 3.3 41.7 - - + +
110B SER* 3.4 15.7 - - - +
111B LEU* 3.4 35.4 - - + +
119B GLY 4.8 2.9 + - - +
139B ILE* 3.8 23.3 - - + -
210B VAL* 4.7 11.0 - - + -
211B ARG 3.1 5.8 - - - +
212B LEU* 3.9 22.0 - - + -
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Residues in contact with VAL 98 (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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96B GLN* 3.8 1.6 - - + +
97B LEU* 1.3 82.7 - - - +
99B THR* 1.3 63.3 + - - +
104B ILE* 4.2 13.2 - - + -
105B HIS 3.0 18.8 - - - +
106B LEU* 4.6 0.4 - - + -
107B HIS* 3.8 8.7 - - - +
168B LEU* 4.2 18.8 - - + -
210B VAL* 3.5 5.2 - - - -
211B ARG* 2.7 62.7 + - + +
212B LEU 4.4 2.5 - - - +
213B MET* 3.6 32.1 - - + -
233B VAL* 4.6 7.0 - - + -
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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