Contacts of the helix formed by residues 142 - 154 (chain A) in PDB entry 5W5T
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 ASP 142 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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58A SER* 3.4 6.8 + - - -
141A MET* 1.3 70.7 - - - +
143A TYR* 1.3 63.6 + - - +
144A GLU* 3.1 13.4 + - - +
145A TYR* 3.3 45.5 + - + +
256A SER* 3.1 19.0 + - - +
258A VAL* 3.5 8.5 - - + +
298A TRP* 3.6 15.1 - - + -
8C GLN* 3.9 8.7 + - - +
12C ARG* 2.8 44.3 + - - -
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Residues in contact with TYR 143 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A ALA* 4.0 2.3 + - - -
54A ASN* 3.3 35.5 + - + +
55A ALA* 3.5 13.9 - - - -
58A SER* 2.8 29.2 + - - +
60A ILE* 4.3 17.3 - - + -
131A VAL* 4.4 15.5 - - + -
133A LEU* 3.4 38.4 - - + +
139A TYR* 2.5 30.8 + - - -
141A MET* 3.9 28.5 - - + -
142A ASP* 1.3 70.1 - - - +
144A GLU* 1.3 62.5 + - - +
145A TYR 3.2 0.7 - - - -
146A MET* 3.0 22.3 + - + +
147A LEU* 3.0 16.7 + - + +
209A ILE* 4.5 5.8 - - + -
256A SER* 5.9 0.2 - - - -
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Residues in contact with GLU 144 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A PRO* 3.5 14.1 - - - +
10A LEU* 2.9 31.7 + - - +
11A ALA* 3.0 34.5 + - - +
58A SER* 4.3 4.8 + - - +
142A ASP* 3.1 16.6 + - - +
143A TYR* 1.3 77.7 - - - +
145A TYR* 1.3 62.1 + - - +
147A LEU* 3.3 7.5 + - - +
148A GLN* 3.0 31.7 + - - +
7C VAL* 3.8 27.3 - - + +
8C GLN* 6.0 0.2 - - - -
9C PRO* 4.3 7.6 - - + +
12C ARG* 3.7 10.2 + - - +
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Residues in contact with TYR 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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142A ASP* 3.3 40.4 + - + +
143A TYR 3.2 0.6 - - - -
144A GLU* 1.3 78.6 - - - +
146A MET* 1.3 57.1 + - - +
148A GLN* 3.3 4.2 + - - +
149A GLN* 3.0 28.4 + - - +
251A HIS* 4.0 7.9 - + + -
255A ASP* 3.7 22.0 - - + -
256A SER* 3.4 25.6 - - - +
7C VAL* 3.7 39.0 - - + +
8C GLN* 3.0 27.0 + - + +
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Residues in contact with MET 146 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141A MET* 4.4 13.0 - - + +
143A TYR* 3.0 17.7 + - + +
145A TYR* 1.3 76.7 - - - +
147A LEU* 1.3 65.3 + - - +
149A GLN* 3.6 2.2 + - - +
150A HIS* 3.1 23.9 + - - +
158A THR* 3.2 33.7 - - + +
159A ILE 3.7 2.0 - - - -
160A GLY* 3.3 24.9 - - - +
209A ILE* 3.8 24.2 - - + +
211A VAL* 3.6 24.7 - - + +
251A HIS* 3.6 38.1 - - + +
256A SER* 4.4 0.9 + - - +
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Residues in contact with LEU 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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10A LEU* 3.4 22.3 - - + +
11A ALA* 3.8 35.0 - - + +
14A ALA* 4.0 9.0 - - + -
60A ILE* 4.9 3.4 - - + -
129A TYR* 3.7 34.1 - - + -
131A VAL* 3.8 17.3 - - + -
143A TYR 3.0 18.2 + - - +
144A GLU* 3.6 13.5 - - - +
146A MET* 1.3 77.8 - - - +
148A GLN* 1.3 60.9 + - - +
150A HIS* 3.2 5.7 + - - +
151A VAL* 3.2 22.3 + - - +
211A VAL* 3.8 18.2 - - + -
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Residues in contact with GLN 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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10A LEU* 3.6 21.0 - - + +
144A GLU* 3.0 23.5 + - - +
145A TYR* 3.7 3.8 - - - +
147A LEU* 1.3 75.3 - - - +
149A GLN* 1.3 65.3 + - - +
151A VAL* 3.6 1.5 - - + +
152A ASP* 3.2 37.0 + - - +
7C VAL* 3.2 55.0 + - - +
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Residues in contact with GLN 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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145A TYR 3.0 16.0 + - - +
146A MET 3.9 4.3 - - - +
148A GLN* 1.3 76.7 - - - +
150A HIS* 1.3 57.5 + - - +
152A ASP* 3.8 3.3 - - - +
153A SER* 2.9 42.6 + - - +
158A THR* 4.0 6.8 - - + +
181A ASP* 5.8 0.4 - - - +
249A VAL* 3.3 20.8 - - - +
250A ALA 2.9 27.9 + - - +
251A HIS* 2.7 37.1 + - - +
255A ASP* 5.4 1.4 - - - +
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Residues in contact with HIS 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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129A TYR* 5.2 2.5 - + - -
146A MET 3.1 14.0 + - - +
147A LEU 3.4 9.0 - - - +
148A GLN 3.2 0.2 - - - -
149A GLN* 1.3 76.9 - - - +
151A VAL* 1.3 66.9 + - + +
153A SER* 3.3 3.9 + - - -
154A GLY* 3.3 18.7 + - - -
155A ALA* 3.3 15.9 + - - +
156A ASP 3.1 23.3 + - - -
157A VAL 3.8 1.6 - - - -
158A THR* 2.8 27.3 + - - +
211A VAL* 3.1 40.3 + - + -
212A PHE* 4.0 0.7 - - - -
213A HIS* 3.3 47.6 + + - -
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Residues in contact with VAL 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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10A LEU* 3.8 22.0 - - + -
129A TYR* 3.6 40.8 - - + +
147A LEU 3.2 11.2 + - - +
148A GLN* 3.6 8.5 - - + +
150A HIS* 1.3 78.4 - - + +
152A ASP* 1.3 79.7 + - - +
153A SER 3.5 0.3 + - - -
154A GLY* 3.7 8.6 + - - -
213A HIS* 4.3 16.2 + - + -
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Residues in contact with ASP 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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148A GLN* 3.2 27.6 + - - +
149A GLN* 4.2 3.6 - - - +
151A VAL* 1.3 92.9 - - - +
153A SER* 1.3 60.0 + - - +
154A GLY 3.4 0.2 - - - -
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Residues in contact with SER 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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149A GLN* 2.9 28.3 + - - -
150A HIS* 3.3 3.1 + - - -
151A VAL 3.3 0.2 - - - -
152A ASP* 1.3 78.2 - - - +
154A GLY* 1.3 61.4 + - - +
155A ALA* 3.1 27.2 + - - +
158A THR* 4.5 1.0 + - - -
247A LYS* 4.3 12.9 + - - -
249A VAL* 4.5 12.6 - - - +
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Residues in contact with GLY 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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150A HIS 3.3 7.0 + - - -
151A VAL* 3.7 7.2 + - - -
152A ASP 3.4 2.8 - - - -
153A SER* 1.3 78.5 + - - +
155A ALA* 1.3 67.1 + - - +
156A ASP* 3.6 3.8 + - - +
213A HIS* 6.0 3.1 - - - -
216A PHE* 6.0 0.7 - - - -
247A LYS* 4.6 6.1 - - - +
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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