Contacts of the helix formed by residues 143 - 155 (chain A) in PDB entry 181L
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 PRO 143 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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139A TYR* 3.1 24.3 - - + +
140A ASN* 3.8 8.3 - - - +
141A GLN 3.3 9.9 - - - +
142A THR* 1.3 89.6 - - - +
144A ASN* 1.3 62.9 + - - +
146A ALA* 3.7 2.6 - - + +
147A LYS* 2.8 55.8 + - - +
173A CL 4.2 4.3 - - + -
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Residues in contact with ASN 144 (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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143A PRO* 1.3 81.4 - - - +
145A ARG* 1.3 62.8 + - - +
147A LYS* 3.5 18.8 + - - +
148A ARG* 3.2 39.4 + - - +
173A CL 3.3 14.6 - - + +
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Residues in contact with ARG 145 (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 LEU* 3.4 17.8 - - - +
10A ASP* 3.7 34.1 + - - +
11A GLU* 2.7 35.9 + - - -
101A ASN* 2.8 29.7 + - - -
105A GLN* 3.5 46.5 + - - +
142A THR* 4.0 9.2 - - - +
144A ASN* 1.3 77.3 - - - +
146A ALA* 1.3 68.7 + - - +
148A ARG* 3.0 30.0 + - - +
149A VAL* 3.1 16.9 + - + +
173A CL 3.3 11.4 - - + +
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Residues in contact with ALA 146 (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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138A TRP* 3.8 30.5 - - + +
139A TYR* 3.7 35.9 - - + -
142A THR* 2.9 20.6 + - - +
143A PRO 3.7 1.1 - - - +
145A ARG* 1.3 77.3 - - - +
147A LYS* 1.3 57.1 + - - +
149A VAL* 3.2 2.8 + - - +
150A ILE* 2.8 35.3 + - - +
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Residues in contact with LYS 147 (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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139A TYR* 3.0 37.9 + - + +
143A PRO* 2.8 35.9 + - - +
144A ASN* 3.6 17.8 + - - +
145A ARG 3.2 0.2 - - - -
146A ALA* 1.3 75.8 - - - +
148A ARG* 1.3 58.9 + - + +
150A ILE* 3.9 5.6 - - - +
151A THR* 3.0 35.1 + - - +
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Residues in contact with ARG 148 (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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9A ILE* 4.7 9.4 + - - +
10A ASP* 2.8 36.7 + - - +
144A ASN* 3.2 28.8 + - - +
145A ARG* 3.0 25.5 + - - +
147A LYS* 1.3 80.5 - - + +
149A VAL* 1.3 59.8 - - - +
151A THR 3.4 0.9 + - - -
152A THR* 2.8 28.3 + - - -
160A ALA* 3.6 37.8 - - + +
161A TYR* 3.6 26.8 - - + +
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Residues in contact with VAL 149 (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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6A MET* 4.7 1.6 - - + -
98A ALA* 3.9 24.1 - - + +
101A ASN* 3.8 25.6 - - + +
102A MET* 4.0 5.2 - - + -
138A TRP* 3.9 25.1 - - + -
145A ARG* 3.1 16.5 + - + +
146A ALA 3.7 5.8 - - - +
148A ARG* 1.3 75.3 - - - +
150A ILE* 1.3 59.2 + - - +
152A THR* 3.2 11.1 + - - -
153A PHE* 3.1 38.0 + - + -
161A TYR* 3.8 15.3 - - - +
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Residues in contact with ILE 150 (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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130A ALA* 3.6 34.7 - - + +
133A LEU* 3.8 29.2 - - + -
134A ALA* 4.0 11.0 - - + +
138A TRP* 3.9 16.6 - - + -
139A TYR* 3.9 29.4 - - + -
146A ALA 2.8 20.0 + - - +
147A LYS* 4.0 4.9 - - - +
149A VAL* 1.3 72.9 - - - +
151A THR* 1.3 62.4 + - - +
153A PHE* 3.2 8.7 + - - +
154A ARG* 2.9 26.2 + - + +
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Residues in contact with THR 151 (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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147A LYS* 3.0 21.2 + - - +
148A ARG 3.7 4.7 - - - -
149A VAL 3.3 0.2 - - - -
150A ILE* 1.3 77.7 - - - +
152A THR* 1.3 59.0 + - - +
154A ARG* 3.2 19.4 + - - +
155A THR* 2.8 51.3 + - + +
157A THR* 5.4 0.7 - - - +
159A ASP* 5.4 4.7 - - + -
160A ALA* 4.0 23.8 - - + +
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Residues in contact with THR 152 (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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6A MET* 4.3 9.0 - - + -
94A VAL* 3.8 30.7 - - + +
95A ARG* 3.8 3.1 - - - +
98A ALA* 3.8 19.3 - - + -
148A ARG 2.8 13.8 + - - -
149A VAL* 3.2 13.7 - - - -
150A ILE 3.1 0.2 - - - -
151A THR* 1.3 81.5 - - - +
153A PHE* 1.3 54.8 + - - +
156A GLY* 2.9 26.9 + - - -
157A THR 4.0 13.7 + - - +
158A TRP* 5.0 3.3 - - + -
160A ALA* 4.5 2.6 - - - +
161A TYR* 3.7 18.5 - - - -
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Residues in contact with PHE 153 (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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91A LEU* 4.3 11.9 - - + -
95A ARG* 2.8 54.3 + - + +
98A ALA* 3.7 11.9 - - + -
99A ALA* 3.6 25.1 - - - -
102A MET* 3.6 24.0 - - - -
121A LEU* 3.6 40.4 - - + -
126A TRP* 3.6 10.7 - - - -
129A ALA* 6.0 0.7 - - + -
130A ALA* 6.1 1.8 - - - +
133A LEU* 3.7 22.2 - - + -
149A VAL* 3.1 26.6 + - + -
150A ILE* 3.2 6.5 + - + +
152A THR* 1.3 77.0 - - - +
154A ARG* 1.3 61.2 + - - +
400A BNZ 4.1 7.9 - + - -
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Residues in contact with ARG 154 (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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95A ARG* 3.5 9.4 + - - -
126A TRP* 3.5 27.5 - - - +
127A ASP* 3.5 31.3 + - - +
130A ALA* 4.0 18.8 - - + +
150A ILE* 2.9 16.8 + - - +
151A THR* 3.7 19.7 + - - +
153A PHE* 1.3 79.9 - - - +
155A THR* 1.3 82.5 + - - +
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Residues in contact with THR 155 (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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95A ARG* 3.5 9.0 + - - -
151A THR* 2.8 29.5 + - + +
154A ARG* 1.3 104.4 - - - +
156A GLY* 1.3 64.8 + - - +
157A THR* 2.7 40.5 + - - +
159A ASP* 5.4 3.1 - - + +
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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