Contacts of the strand formed by residues 162 - 167 (chain A) in PDB entry 1LNU
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 TYR 162 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106A LEU* 4.1 19.1 - - + -
122A TRP* 5.5 1.8 - - + -
123A LEU 3.0 7.9 - - - +
124A ARG* 3.1 53.3 + - + -
125A ASN 4.5 0.4 - - - +
152A LEU* 4.3 16.4 - - + -
154A PHE* 3.4 41.6 - + + +
155A ILE 3.6 11.3 + - - -
156A PRO* 5.7 1.1 - - + -
160A ASP* 3.8 22.9 + - - -
161A ILE* 1.3 88.8 - - - +
163A ASP* 1.3 64.0 + - - +
178A HIS* 3.0 25.7 - - - -
179A TRP* 3.2 41.4 + + + +
181A PRO* 5.7 1.1 - - + -
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Residues in contact with ASP 163 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122A TRP* 4.4 2.0 - - - -
123A LEU* 2.7 54.9 + - + +
126A SER 6.1 0.7 - - - +
161A ILE* 5.4 0.5 - - - +
162A TYR* 1.3 77.6 - - - +
164A CYS* 1.3 61.2 + - - +
176A LEU* 3.6 29.8 - - + +
177A LYS 2.7 33.0 - - - +
178A HIS* 2.8 29.6 + - - +
179A TRP 5.0 0.2 - - - +
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Residues in contact with CYS 164 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92A VAL* 3.7 12.1 - - + +
108A CYS* 2.0 50.7 - - - -
120A ILE* 3.5 21.8 - - - -
121A THR 4.5 0.4 - - - -
122A TRP* 3.2 28.6 - - + -
163A ASP* 1.3 70.2 - - - +
165A LYS* 1.3 59.7 + - - +
166A VAL* 3.9 5.1 + - - +
175A VAL 3.5 5.2 - - - +
176A LEU* 3.8 2.5 - - - -
177A LYS* 3.0 33.0 + - + +
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Residues in contact with LYS 165 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119A ASN 3.4 1.2 - - - +
120A ILE* 3.2 5.9 - - - -
121A THR* 2.6 63.2 + - - +
123A LEU* 3.6 28.2 - - + +
128A SER* 5.6 1.3 - - - +
163A ASP 3.4 0.4 + - - -
164A CYS* 1.3 71.5 - - - +
166A VAL* 1.3 61.5 + - - +
167A GLU* 4.6 13.5 - - + +
174A PRO* 3.7 32.0 - - + +
175A VAL 3.8 2.7 - - - -
176A LEU* 3.9 18.7 - - + +
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Residues in contact with VAL 166 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A PRO* 4.3 10.1 - - + -
89A GLN 5.2 1.6 - - - +
90A ALA* 4.7 12.3 - - + -
110A VAL* 4.1 25.4 - - + -
118A ILE* 3.9 24.7 - - + -
119A ASN 3.4 2.0 - - - -
120A ILE* 4.3 13.0 - - + -
164A CYS* 4.6 9.0 - - - +
165A LYS* 1.3 77.8 - - - +
167A GLU* 1.3 66.7 + - - +
171A LEU* 3.4 15.7 - - + +
174A PRO* 3.1 5.9 - - - +
175A VAL* 2.8 48.8 + - + +
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Residues in contact with GLU 167 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118A ILE* 3.3 5.6 - - - +
119A ASN* 3.0 42.0 + - + +
121A THR* 4.5 15.1 + - - +
165A LYS* 4.6 13.3 - - + +
166A VAL* 1.3 80.5 - - - +
168A HIS* 1.3 60.6 + - - +
171A LEU* 3.6 5.6 - - + -
174A PRO* 4.1 20.7 - - + +
302A NAG 2.8 53.9 - - + +
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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