Contacts of the helix formed by residues 132 - 143 (chain A) in PDB entry 3LEZ
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 LEU 132 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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95A VAL* 4.1 21.7 - - + +
99A LYS* 4.3 17.5 - - + +
103A GLU* 3.7 20.4 - - + +
104A LEU* 3.6 18.7 + - + +
106A GLU 3.9 3.8 + - - -
108A ILE* 4.3 18.5 - - + +
130A MET 4.1 0.2 + - - -
131A THR* 1.3 73.2 - - - +
133A VAL* 1.3 59.0 + - - +
135A ILE* 3.6 15.3 - - + +
136A ALA* 2.8 29.6 + - - +
150A LEU 4.7 4.0 - - - +
151A LEU* 4.2 18.9 - - + +
154A ALA* 3.8 29.6 - - + -
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Residues in contact with VAL 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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96A LEU* 5.2 7.0 - - + -
104A LEU* 3.7 40.3 + - + +
105A GLU* 6.3 0.2 - - + -
131A THR* 3.2 7.2 + - - +
132A LEU* 1.3 74.3 - - - +
134A GLU* 1.3 62.3 + - + +
136A ALA* 3.3 6.5 + - - +
137A ASP* 2.9 25.3 + - + +
219A VAL* 4.7 10.8 - - + -
223A MET* 3.5 18.8 - - + +
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Residues in contact with GLU 134 (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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121A ILE* 5.5 0.2 - - - +
129A GLY 4.9 0.2 - - - +
130A MET* 3.5 26.3 - - + +
131A THR* 3.0 43.2 + - - +
133A VAL* 1.3 77.5 - - + +
135A ILE* 1.3 61.7 + - - +
137A ASP* 3.3 7.8 + - - +
138A ALA* 3.0 23.4 + - - +
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Residues in contact with ILE 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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108A ILE* 3.9 30.7 - - + +
122A THR* 5.2 0.4 - - + -
130A MET* 3.8 26.2 - - + +
131A THR 2.8 21.0 + - - +
132A LEU* 3.6 9.6 - - + +
134A GLU* 1.3 73.5 - - - +
136A ALA* 1.3 65.0 + - - +
138A ALA* 3.2 2.6 + - - -
139A ALA* 2.9 20.3 + - - +
147A ALA* 3.4 35.7 - - - +
150A LEU* 3.8 32.8 - - + -
151A LEU* 3.9 15.0 - - + +
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Residues in contact with ALA 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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92A VAL* 3.5 39.3 - - + -
95A VAL* 6.1 1.8 - - + -
96A LEU* 6.3 1.1 - - + -
132A LEU 2.8 21.0 + - - +
133A VAL* 3.4 7.9 - - - +
135A ILE* 1.3 74.0 - - - +
137A ASP* 1.3 62.3 + - - +
139A ALA* 3.3 1.6 + - - +
140A ILE* 3.0 28.6 + - - +
151A LEU* 4.3 8.3 - - + +
223A MET* 3.9 10.3 - - + -
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Residues in contact with ASP 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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133A VAL* 2.9 14.4 + - + +
134A GLU* 3.5 11.9 - - - +
135A ILE 3.3 0.2 - - - -
136A ALA* 1.3 76.1 - - - +
138A ALA* 1.3 57.3 + - - +
141A ARG* 2.9 77.4 + - - +
142A TYR* 4.7 3.1 - - - -
223A MET* 3.6 25.6 - - + +
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Residues in contact with ALA 138 (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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121A ILE* 3.7 34.1 - - + -
122A THR* 5.1 0.4 - - + -
130A MET* 4.4 4.5 - - + -
134A GLU 3.0 15.9 + - - +
135A ILE 3.6 4.5 - - - +
137A ASP* 1.3 77.1 + - - +
139A ALA* 1.3 62.5 + - - +
142A TYR* 3.2 28.1 + - - +
144A ASP* 3.2 22.8 + - + +
147A ALA* 4.1 5.2 - - + -
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Residues in contact with ALA 139 (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 LYS* 3.6 16.3 - - + +
135A ILE 2.9 16.8 + - - +
136A ALA 3.7 2.5 - - - +
138A ALA* 1.3 76.4 - - - +
140A ILE* 1.3 59.1 + - + +
143A SER* 3.1 23.9 + - - -
144A ASP 4.0 6.5 - - - +
147A ALA* 3.7 14.9 - - + +
148A GLY 4.2 5.6 - - - +
151A LEU* 3.6 27.4 - - + -
247A LYS* 3.4 8.8 - - - -
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Residues in contact with ILE 140 (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 LYS 4.5 0.4 - - - -
89A PRO* 3.9 21.3 - - + -
92A VAL* 3.7 25.6 - - + -
136A ALA 3.0 13.2 + - - +
137A ASP 4.3 0.9 - - - +
139A ALA* 1.3 79.0 - - - +
141A ARG* 1.3 62.3 + - - +
142A TYR 3.6 0.2 + - - -
143A SER 4.1 1.0 + - - -
220A LEU* 3.6 31.0 - - + -
223A MET* 3.8 44.4 - - + +
224A LEU* 4.0 17.3 - - + -
227A ASN* 3.2 12.3 - - + +
246A ASP 4.7 2.0 - - - +
247A LYS* 3.5 22.2 - - + +
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Residues in contact with ARG 141 (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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137A ASP* 2.9 55.3 + - - +
140A ILE* 1.3 73.7 - - - +
142A TYR* 1.3 87.2 + - + +
223A MET* 3.4 31.0 - - + +
226A ASN* 3.0 35.4 + - - +
227A ASN* 3.2 8.7 - - - +
228A THR* 2.7 44.9 + - + +
229A THR* 3.9 1.0 - - - +
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Residues in contact with TYR 142 (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 TYR* 3.5 20.5 + - - +
120A PRO* 4.6 9.0 - - + -
121A ILE* 3.7 39.7 - - + -
137A ASP* 4.7 2.5 - - - -
138A ALA* 3.2 16.4 + - - +
141A ARG* 1.3 115.5 + - + +
143A SER* 1.3 71.2 + - - +
144A ASP 3.4 2.4 + - - +
228A THR* 3.6 27.6 - - + +
229A THR* 4.2 9.9 - - + +
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Residues in contact with SER 143 (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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85A SER* 3.0 20.6 + - - -
88A LYS* 3.3 8.2 + - - +
118A TYR* 3.9 11.6 - - - -
139A ALA 3.1 18.9 + - - -
140A ILE 4.1 1.2 + - - -
141A ARG 3.8 1.0 - - - -
142A TYR* 1.3 80.6 - - - +
144A ASP* 1.3 65.8 + - - +
145A ASN* 3.2 6.4 + - - +
229A THR* 4.6 2.7 - - - -
247A LYS* 2.9 21.0 + - - -
305A EPE 3.0 31.9 + - - -
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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