Contacts of the strand formed by residues 130 - 137 (chain A) in PDB entry 2LHS
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 GLN 130 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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80A THR* 5.9 0.4 - - - +
81A TRP 3.3 9.9 - - - +
82A LYS* 2.9 42.5 + - + +
83A LEU* 4.2 0.4 - - - -
128A ALA* 2.9 27.5 + - + +
129A ALA* 1.3 84.1 - - + +
131A VAL* 1.3 69.8 + - - +
132A THR* 4.1 3.4 - - + +
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Residues in contact with VAL 131 (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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79A PHE 3.4 1.2 - - - +
80A THR* 5.4 0.2 - - - -
81A TRP* 2.9 42.9 + - + -
83A LEU* 3.8 5.4 - - + -
92A TRP* 3.7 44.9 - - + +
127A PRO* 3.8 24.2 - - + -
130A GLN* 1.3 80.1 - - - +
132A THR* 1.3 58.2 + - - +
133A HIS* 3.7 31.6 + - + +
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Residues in contact with THR 132 (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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78A SER* 5.4 4.0 - - - -
79A PHE 3.5 6.2 + - - -
80A THR* 4.1 15.5 - - - +
130A GLN* 4.1 3.6 - - + +
131A VAL* 1.3 74.3 - - - +
133A HIS* 1.3 76.6 + - - +
134A GLN* 5.7 1.7 - - - +
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Residues in contact with HIS 133 (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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78A SER* 3.7 0.3 - - - -
79A PHE* 2.8 39.4 + - + +
81A TRP* 5.6 1.3 - + + -
92A TRP* 4.3 20.3 + + + -
94A TYR* 4.7 6.7 - - - +
120A PHE* 3.9 31.8 - + + +
122A ASP* 4.4 8.3 + - - -
131A VAL* 3.7 24.2 - - + +
132A THR* 1.3 97.1 + - - +
134A GLN* 1.3 72.2 + - - +
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Residues in contact with GLN 134 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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76A PRO* 5.1 12.3 - - + +
77A ASN 3.3 19.3 + - - +
78A SER* 4.1 12.6 - - - -
79A PHE* 4.2 1.6 - - - -
120A PHE* 3.5 15.8 - - - -
132A THR* 5.7 1.6 - - - +
133A HIS* 1.3 80.9 - - - +
135A CYS* 1.3 64.6 + - - +
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Residues in contact with CYS 135 (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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75A GLY 3.7 0.3 - - - +
76A PRO* 3.5 0.2 - - - +
77A ASN 2.8 30.6 + - - +
79A PHE* 3.5 25.6 - - + -
94A TYR* 4.6 2.5 - - + -
117A PHE* 3.4 17.5 - - - -
118A CYS* 2.0 52.9 - - + -
120A PHE* 3.9 11.7 - - + -
134A GLN* 1.3 77.6 - - - +
136A ASN* 1.3 64.5 + - - +
137A ILE 3.9 0.3 + - - -
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Residues in contact with ASN 136 (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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75A GLY* 3.4 10.8 - - - -
76A PRO* 3.3 31.2 - - - +
117A PHE* 3.4 16.8 - - - +
118A CYS* 3.5 6.1 - - - -
135A CYS* 1.3 79.8 - - - +
137A ILE* 1.3 65.0 + - - +
138A PRO* 3.6 1.7 - - - +
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Residues in contact with ILE 137 (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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7A PRO* 6.5 0.7 - - + -
72A LEU* 5.8 3.4 - - + -
73A LYS 4.1 4.9 - - - +
74A THR* 4.3 1.3 - - - -
75A GLY* 2.9 36.0 + - - +
77A ASN* 3.5 35.0 - - + +
79A PHE* 4.3 15.5 - - + -
96A ILE* 5.4 1.1 - - + -
117A PHE* 3.7 16.4 - - + -
136A ASN* 1.3 73.6 - - - +
138A PRO* 1.4 79.4 - - + +
139A ALA* 3.6 1.0 + - - +
141A ARG* 5.0 4.0 - - + +
145A HIS* 5.2 0.4 - - - +
147A ILE* 4.2 26.5 - - + -
168A LEU* 3.7 28.0 - - + -
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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