Contacts of the helix formed by residues 135 - 147 (chain A) in PDB entry 4NWO
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 135 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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133A PRO* 3.3 4.8 - - + +
134A GLY* 1.3 74.7 - - - +
136A PRO* 1.3 73.1 - - - +
137A ALA* 3.0 37.6 + - - +
138A SER* 3.1 30.0 + - - +
139A ILE* 3.2 15.0 + - - +
12B ASN* 5.1 0.3 + - - -
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Residues in contact with PRO 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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23A ILE* 3.7 35.7 - - + +
24A SER* 3.5 21.8 - - - +
27A ALA* 4.7 7.5 - - + +
134A GLY 3.2 6.7 - - - +
135A ASP* 1.3 89.2 - - - +
137A ALA* 1.3 60.6 + - - +
139A ILE* 3.4 24.7 - - + +
140A SER* 4.5 1.9 + - - -
21B ILE* 6.1 0.7 - - - +
25B LEU* 5.7 5.8 - - + +
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Residues in contact with ALA 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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135A ASP* 3.0 14.6 + - - +
136A PRO* 1.3 81.1 - - - +
138A SER* 1.3 59.7 + - - +
139A ILE 3.4 0.5 + - - -
140A SER* 3.8 15.1 + - - -
141A ASP* 4.4 5.2 - - - +
10B THR 5.7 3.6 - - - +
11B VAL* 6.0 0.9 - - - -
12B ASN* 3.4 33.2 + - - +
109B SER* 4.8 13.5 - - - +
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Residues in contact with SER 138 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107A SER* 6.0 1.3 - - - -
133A PRO* 3.9 19.5 - - - -
135A ASP* 3.1 27.4 + - - +
137A ALA* 1.3 75.1 - - - +
139A ILE* 1.3 65.2 + - - +
140A SER 3.4 0.4 - - - -
141A ASP* 3.5 7.7 + - - +
142A CYS* 3.1 29.8 + - - +
12B ASN* 4.4 10.2 + - - +
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Residues in contact with ILE 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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24A SER* 4.4 8.7 - - - +
27A ALA* 4.4 7.9 - - + +
28A ILE* 3.7 35.2 - - + +
31A ALA* 5.8 0.9 - - + -
73A THR* 3.7 14.8 - - - +
132A LEU* 4.1 20.4 - - + +
133A PRO* 3.2 27.6 - - - +
134A GLY 4.8 0.7 - - - +
135A ASP 3.2 13.9 + - - +
136A PRO* 3.4 19.5 - - + +
137A ALA 3.2 0.6 - - - -
138A SER* 1.3 78.7 - - - +
140A SER* 1.3 64.4 + - - +
142A CYS* 3.7 4.7 - - - +
143A LEU* 3.0 27.3 + - + +
21B ILE* 6.3 0.7 - - + -
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Residues in contact with SER 140 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A ALA* 5.7 2.7 - - - -
35A TYR* 4.1 4.2 + - - -
136A PRO 4.5 1.7 + - - -
137A ALA 3.8 11.3 + - - -
139A ILE* 1.3 79.9 - - - +
141A ASP* 1.3 70.2 + - - +
143A LEU* 3.9 3.6 - - - +
144A LEU* 2.9 32.4 + - - +
15B THR* 6.1 0.2 - - - -
17B THR* 4.0 18.0 + - - -
18B SER* 3.6 27.3 - - - -
21B ILE* 4.5 17.5 - - - -
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Residues in contact with ASP 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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106A GLU* 5.7 2.4 - - - +
137A ALA 4.4 3.1 - - - +
138A SER* 3.5 10.1 + - - +
139A ILE 3.3 0.2 - - - -
140A SER* 1.3 88.2 + - - +
142A CYS* 1.3 62.5 + - - +
144A LEU* 3.7 12.2 + - - +
145A ALA* 3.4 21.7 + - - +
12B ASN* 3.5 26.5 + - - +
13B SER* 2.5 34.3 + - - -
15B THR* 4.5 3.5 + - - +
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Residues in contact with CYS 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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103A MET* 4.0 30.2 - - - +
107A SER* 4.7 13.0 - - - -
119A GLN* 4.6 3.1 - - - -
132A LEU* 3.9 17.9 - - + -
133A PRO* 3.7 26.9 - - + -
138A SER* 3.1 23.1 + - - +
139A ILE 3.7 3.4 - - - +
141A ASP* 1.3 75.8 - - - +
143A LEU* 1.3 65.4 + - - +
145A ALA* 3.3 12.7 + - - +
146A VAL* 3.4 16.8 + - - +
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Residues in contact with LEU 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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28A ILE* 4.4 19.1 - - + -
31A ALA* 4.1 25.1 - - + -
32A LEU* 4.7 8.7 - - + -
35A TYR* 4.1 14.6 - - + +
71A VAL* 4.9 12.6 - - + -
130A VAL* 5.8 2.0 - - + -
132A LEU* 3.7 28.9 - - + +
139A ILE* 3.0 16.9 + - + +
140A SER* 3.9 4.0 - - - +
142A CYS* 1.3 75.2 - - - +
144A LEU* 1.3 56.9 + - - +
145A ALA 3.1 0.3 + - - -
146A VAL* 3.2 10.5 + - + -
147A PHE* 2.8 57.8 + - + +
150A ILE* 5.0 4.9 - - + -
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Residues in contact with LEU 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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35A TYR* 3.7 12.0 + - - +
140A SER 2.9 18.3 + - - +
141A ASP* 3.9 12.6 - - - +
143A LEU* 1.3 75.7 - - - +
145A ALA* 1.3 60.4 + - - +
148A PRO* 3.2 18.3 - - + +
168A MET 4.5 11.2 - - - +
169A ILE* 4.2 23.1 - - + -
15B THR* 3.6 37.5 - - + +
17B THR* 4.7 7.6 - - + +
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Residues in contact with ALA 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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102A LEU* 3.6 27.4 - - + +
103A MET* 4.9 5.6 - - + -
106A GLU* 4.9 14.8 - - + -
141A ASP 3.4 10.8 + - - +
142A CYS* 3.3 11.6 + - - +
143A LEU 3.1 1.0 - - - -
144A LEU* 1.3 81.0 - - - +
146A VAL* 1.3 65.2 + - + +
147A PHE 3.7 0.2 - - - -
148A PRO* 3.8 7.4 - - - +
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Residues in contact with VAL 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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99A PHE* 3.7 45.0 - - + +
102A LEU* 4.5 10.1 - - + -
103A MET* 3.9 28.5 - - + -
130A VAL* 4.7 10.1 - - + -
132A LEU* 5.4 0.7 - - + -
142A CYS 3.5 12.3 - - - +
143A LEU* 3.8 12.3 - - + +
145A ALA* 1.3 79.3 - - + +
147A PHE* 1.3 69.3 + - - +
148A PRO* 3.3 3.1 - - - -
149A ALA* 3.1 20.0 + - - +
150A ILE* 3.6 15.3 - - + +
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Residues in contact with PHE 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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6A ILE* 6.0 0.2 - - + -
32A LEU* 4.0 18.8 - - + -
35A TYR* 4.0 21.8 - + + -
36A LEU* 3.8 23.3 - - + -
69A LEU* 4.4 8.1 - - + -
143A LEU* 2.8 35.6 + - + +
146A VAL* 1.3 69.3 - - - +
148A PRO* 1.4 63.7 - - + +
149A ALA 2.9 7.4 + - - -
150A ILE* 3.0 32.4 + - + -
151A PRO* 3.0 33.8 - - + +
162A LEU* 4.9 6.3 - - + -
164A CYS* 3.9 24.9 - - - -
169A ILE* 3.5 27.1 - - + -
171A PRO* 5.8 0.7 - - + -
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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