Contacts of the strand formed by residues 139 - 142 (chain B) in PDB entry 1LVB
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 PHE 139 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81B ASP* 4.5 6.7 - - + -
134B SER* 2.8 34.2 + - - +
137B GLY 3.8 1.1 - - - +
138B ILE* 1.3 82.8 - - + +
140B TRP* 1.3 64.6 - - - +
168B SER* 3.8 15.3 - - - -
169B ALA* 5.3 1.8 - - + -
178B TYR* 4.1 28.9 - - + -
179B PHE 3.4 14.1 - - - -
180B THR* 3.5 22.0 - - + -
211B TRP* 3.3 40.8 - + + -
212B GLY* 4.3 3.3 - - - +
214B HIS* 4.1 15.7 - + + -
216B VAL* 4.2 25.1 - - + -
304D LEU* 4.8 3.1 - - + -
306D PHE* 4.4 11.7 - + - -
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Residues in contact with TRP 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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103B PRO* 3.8 31.5 - - + +
104B GLN 3.7 34.5 - - - -
105B ARG* 3.8 9.0 - - + -
131B THR* 3.4 32.8 - - + +
132B PHE 3.3 4.7 - - - -
133B PRO* 3.4 44.3 - - + +
137B GLY* 3.1 29.0 + - - -
139B PHE* 1.3 75.1 - - - +
141B LYS* 1.3 62.7 + - - +
178B TYR* 3.2 6.2 - - - -
179B PHE* 2.9 54.6 + + + -
181B SER* 3.8 17.0 - - - -
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Residues in contact with LYS 141 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131B THR* 2.5 35.5 + - - -
132B PHE* 2.7 26.1 + - + +
133B PRO 5.3 0.7 - - - +
134B SER* 4.2 12.1 - - - +
140B TRP* 1.3 72.3 - - - +
142B HIS* 1.3 57.1 + - - +
143B TRP* 3.6 29.1 - - + -
176B ASN* 3.3 29.3 + - - +
177B ASN 3.3 7.0 - - - +
178B TYR* 3.0 41.6 + - + +
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Residues in contact with HIS 142 (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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109B ILE* 4.0 16.6 - - + -
129B SER* 4.3 1.6 - - - +
130B CYS 3.7 15.0 - - - +
131B THR* 4.3 0.2 - - - +
141B LYS* 1.3 77.0 - - - +
143B TRP* 1.3 68.3 + - - +
144B ILE* 3.1 48.8 + - + +
146B THR* 3.8 8.9 - - - +
155B LEU* 4.3 14.7 - - + +
167B HIS* 3.2 27.6 - + - -
177B ASN* 2.8 57.4 + - + +
178B TYR 3.9 3.1 - - - -
179B PHE* 3.8 16.9 + - + -
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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
------------------------------------------------------------
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