Contacts of the strand formed by residues 115 - 121 (chain A) in PDB entry 4LHZ
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 GLU 115 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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82A MET 3.3 12.3 + - - +
83A GLY* 3.2 2.3 - - - -
84A ILE 3.0 25.5 + - - -
113A ASP* 3.4 10.5 + - - +
114A VAL* 1.3 80.7 - - - +
116A LYS* 1.3 64.8 + - - +
165A LEU* 3.8 17.7 - - + -
168A ASP* 3.8 47.4 - - + +
169A ILE* 4.3 6.1 - - + -
172A LYS* 4.5 10.5 - - - +
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Residues in contact with LYS 116 (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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84A ILE* 3.6 8.5 - - + +
86A LEU* 4.5 4.7 - - + -
103A ILE* 5.7 9.9 - - + +
106A ILE* 3.6 29.8 - - + -
112A ALA 5.9 0.4 + - - -
113A ASP 5.3 0.4 - - - -
114A VAL* 2.9 40.4 + - + +
115A GLU* 1.3 83.4 - - - +
117A MET* 1.3 63.2 + - - +
143A TYR 5.6 0.9 - - - -
145A ILE* 3.9 43.0 - - + +
146A LYS* 4.0 9.2 + - - +
165A LEU* 5.2 2.3 - - - +
168A ASP* 5.8 0.3 - - - +
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Residues in contact with MET 117 (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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84A ILE 3.2 7.5 + - - +
85A MET* 3.4 23.6 - - - +
86A LEU* 2.8 36.4 + - - +
116A LYS* 1.3 76.4 - - - +
118A ILE* 1.3 59.0 + - - +
119A LEU* 3.3 26.1 + - + -
145A ILE* 4.1 0.4 - - - -
146A LYS* 3.5 23.1 - - + +
147A PHE 5.0 0.4 - - - -
148A MET* 3.3 39.9 - - + -
161A ALA* 3.5 27.8 - - + +
164A THR* 4.3 14.4 - - + -
165A LEU* 4.4 13.2 - - + -
168A ASP* 6.1 0.2 - - - +
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Residues in contact with ILE 118 (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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86A LEU* 3.3 10.1 - - + +
88A TYR* 3.7 31.9 - - + -
96A PHE* 5.2 1.3 - - + -
99A ILE* 4.0 27.4 - - + -
103A ILE* 4.9 4.5 - - + -
117A MET* 1.3 69.6 - - - +
119A LEU* 1.3 59.3 + - - +
136A GLY 5.1 0.9 - - - +
139A LEU* 4.0 14.1 - - + -
140A ALA* 3.8 31.9 - - + +
143A TYR* 5.4 0.7 - - + -
145A ILE* 3.3 24.9 - - + +
146A LYS 2.9 10.6 + - - +
147A PHE* 3.1 11.2 - - + -
148A MET 2.8 31.9 + - - -
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Residues in contact with LEU 119 (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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24A VAL* 4.7 20.4 - - + -
85A MET* 3.6 34.1 - - + -
86A LEU 2.5 15.5 + - - +
87A VAL* 3.2 16.9 - - + +
88A TYR* 2.9 29.1 + - - -
117A MET* 3.3 35.9 - - + +
118A ILE* 1.3 73.5 - - - +
120A GLY* 1.3 60.2 + - - +
121A ASN* 3.3 4.1 + - + -
148A MET* 3.4 15.0 - - + +
150A THR* 4.2 14.6 - - + +
158A VAL* 6.0 1.1 - - + -
161A ALA* 3.7 13.5 - - + -
162A PHE* 5.6 2.5 - - + -
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Residues in contact with GLY 120 (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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88A TYR* 3.6 31.2 - - - -
90A ILE* 4.0 6.9 - - - +
118A ILE 3.9 1.8 + - - -
119A LEU* 1.3 68.6 - - - +
121A ASN* 1.3 62.6 + - - -
123A CYS 4.2 0.7 + - - -
147A PHE* 4.4 3.4 - - - -
148A MET 2.6 13.4 + - - -
149A GLU* 3.2 10.4 - - - +
150A THR* 2.9 26.3 + - - +
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Residues in contact with ASN 121 (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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19A VAL 3.0 23.0 + - - +
20A GLY 3.5 13.5 + - - -
24A VAL* 3.8 8.4 - - + +
87A VAL* 4.1 10.5 - - + -
88A TYR 2.7 20.7 + - - +
89A ASP* 3.7 0.2 - - - -
90A ILE* 3.1 22.7 + - - +
119A LEU* 3.3 2.0 + - + +
120A GLY* 1.3 71.4 - - - +
122A LYS* 1.3 82.4 + - - +
123A CYS 3.3 2.5 + - - -
150A THR* 2.4 36.1 - - + +
152A ALA 3.5 8.2 + - - +
201A GTP 3.2 23.2 + - - -
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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