Contacts of the strand formed by residues 148 - 153 (chain B) in PDB entry 3EBL
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 VAL 148 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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80B ILE* 4.1 17.5 - - + -
81B TYR 3.5 9.2 - - - +
82B ARG* 4.3 15.0 - - + -
113B PHE* 3.6 28.5 - - + -
114B PRO 2.9 5.9 + - - +
115B VAL* 3.3 6.6 - - + +
116B ILE* 2.7 33.1 + - - +
147B GLY* 1.3 77.6 - - - +
149B VAL* 1.3 64.8 + - - +
150B VAL* 4.2 3.1 - - + -
181B PHE 5.9 0.4 - - - +
182B MET* 3.8 26.5 - - + -
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Residues in contact with VAL 149 (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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79B ARG 3.6 1.3 - - - +
80B ILE* 3.3 4.9 - - - +
81B TYR* 2.7 50.0 + - + +
116B ILE* 3.3 23.3 - - + +
118B PHE* 4.2 12.3 - - + -
138B CYS* 3.7 41.1 - - + +
141B PHE* 3.8 17.5 - - + -
142B VAL* 3.6 20.4 - - + +
145B SER* 5.0 0.7 - - - +
148B VAL* 1.3 76.8 - - - +
150B VAL* 1.3 66.7 + - - +
151B SER 4.0 0.2 - - - -
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Residues in contact with VAL 150 (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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78B VAL* 3.8 35.0 - - + -
79B ARG 3.6 2.7 - - - -
80B ILE* 4.3 6.1 - - + -
115B VAL* 4.5 7.2 - - + -
116B ILE 2.8 10.8 + - - +
117B ILE* 3.4 9.6 - - + +
118B PHE 2.9 23.8 + - - +
148B VAL* 4.2 6.7 - - + -
149B VAL* 1.3 75.9 - - - +
151B SER* 1.3 61.5 + - - +
152B VAL* 3.7 6.5 + - + -
172B ALA* 5.5 0.9 - - + -
175B TRP* 4.6 2.9 - - + -
176B VAL* 4.1 25.6 - - + -
182B MET* 3.9 28.0 - - + -
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Residues in contact with SER 151 (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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78B VAL* 3.1 5.7 - - - -
79B ARG 2.8 43.9 + - - -
81B TYR* 3.9 8.5 - - - -
118B PHE* 3.4 23.9 + - - -
120B HIS* 5.0 3.1 + - - +
129B ALA* 3.7 26.0 + - - +
134B TYR* 5.4 1.4 - - - +
138B CYS* 3.9 24.0 - - - -
149B VAL 4.0 0.2 - - - -
150B VAL* 1.3 72.5 - - - +
152B VAL* 1.3 62.7 + - - +
153B ASN 3.7 0.5 + - - -
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Residues in contact with VAL 152 (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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76B LEU* 4.1 16.4 - - + -
77B GLU 4.2 3.1 - - - +
78B VAL* 4.1 9.2 - - + -
117B ILE* 3.7 22.4 - - + -
118B PHE 3.0 9.9 + - - +
119B PHE* 3.7 26.0 - - + -
120B HIS* 3.8 9.9 + - - -
129B ALA* 4.4 2.9 - - - +
150B VAL* 4.0 3.6 - - + +
151B SER* 1.3 74.8 + - - +
153B ASN* 1.3 60.9 + - - +
154B TYR* 3.0 33.9 + - + +
168B ASP 4.3 4.9 - - - +
172B ALA* 3.5 31.6 - - + -
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Residues in contact with ASN 153 (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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75B GLY 5.7 0.2 - - - +
76B LEU* 3.4 14.7 - - - +
77B GLU* 2.9 42.3 + - + +
78B VAL 5.8 0.2 - - - -
120B HIS* 4.8 2.7 - - - -
128B SER* 3.0 17.8 + - - -
129B ALA* 2.7 39.4 + - + +
151B SER 3.7 1.6 + - - -
152B VAL* 1.3 68.2 - - - +
154B TYR* 1.3 67.1 + - - +
155B ARG* 5.5 0.7 - - - +
156B ARG* 6.4 0.4 - - - -
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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