Contacts of the helix formed by residues 142 - 157 (chain A) in PDB entry 4L1O
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 SER 142 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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50A ASP* 3.4 25.9 - - - +
113A TRP* 3.6 28.7 - - - +
116A PRO* 3.3 25.6 - - - +
139A SER* 3.3 14.3 + - - -
141A LEU* 1.3 73.8 - - - +
143A GLU* 1.3 63.5 + - - +
144A ASN 3.3 2.6 + - - -
145A MET* 4.6 0.5 - - - +
146A ALA* 3.1 20.6 + - - +
285A ILE* 4.2 2.5 - - - -
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Residues in contact with GLU 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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50A ASP* 3.3 4.6 + - - +
140A GLU* 3.6 15.2 - - - +
141A LEU 3.2 5.8 + - - +
142A SER* 1.3 73.5 - - - +
144A ASN* 1.3 68.8 + - - +
146A ALA* 3.4 6.4 - - - +
147A SER* 3.1 32.8 + - - +
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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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46A ALA* 3.8 20.1 - - + +
49A ALA* 3.5 26.7 + - - +
50A ASP* 2.8 28.6 + - - +
143A GLU* 1.3 81.0 - - - +
145A MET* 1.3 61.6 + - - +
147A SER* 3.4 6.4 + - - -
148A LEU* 2.9 28.9 + - - +
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Residues in contact with MET 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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43A LEU* 3.9 35.0 - - + +
46A ALA* 3.8 9.3 - - + +
47A LEU* 3.5 37.9 - - + -
50A ASP* 2.9 17.7 + - - +
116A PRO* 3.8 33.9 - - + +
117A PHE* 4.0 18.4 - - + -
138A PRO* 6.5 0.2 - - + -
142A SER 3.9 3.4 - - - +
144A ASN* 1.3 71.9 - - - +
146A ALA* 1.3 67.0 + - - +
148A LEU* 4.3 6.5 - - - -
149A LEU* 2.8 40.1 + - + +
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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 PRO* 4.1 25.6 - - + +
139A SER 3.8 17.2 + - - +
140A GLU* 4.8 3.6 - - - -
142A SER* 3.1 14.0 + - - +
143A GLU* 3.4 12.8 - - - +
145A MET* 1.3 76.1 - - - +
147A SER* 1.3 61.6 + - - +
149A LEU* 3.5 2.1 + - - +
150A ALA* 3.1 24.0 + - - +
164A VAL* 5.0 0.3 - - - +
166A ASN* 5.0 1.5 - - - +
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Residues in contact with SER 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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143A GLU* 3.1 17.5 + - - +
144A ASN* 3.6 9.6 - - - -
146A ALA* 1.3 75.0 - - - +
148A LEU* 1.3 68.1 + - - +
150A ALA* 3.4 7.8 + - - +
151A THR* 3.2 23.7 + - - -
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Residues in contact with LEU 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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39A GLN* 4.6 0.4 - - - +
42A GLU* 3.2 50.5 - - + +
43A LEU* 3.8 23.8 - - + -
46A ALA* 4.0 10.1 - - + -
144A ASN 2.9 18.0 + - - +
145A MET* 3.7 7.2 - - - +
147A SER* 1.3 75.4 - - - +
149A LEU* 1.3 60.1 + - - +
151A THR* 2.9 10.1 + - + -
152A ILE* 2.9 57.9 + - + +
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Residues in contact with LEU 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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116A PRO 4.0 2.5 - - - +
117A PHE* 4.1 25.6 - - + -
120A THR* 3.6 31.6 - - + +
121A ILE* 4.2 15.7 - - + -
136A LEU* 4.5 7.4 - - + -
138A PRO* 4.7 14.1 - - + -
145A MET* 2.8 44.1 + - + +
146A ALA 3.9 2.7 - - - +
148A LEU* 1.3 73.2 - - - +
150A ALA* 1.3 63.0 + - - +
152A ILE* 4.0 14.4 - - + -
153A ILE* 3.0 43.4 + - + +
164A VAL* 3.8 2.1 - - + +
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Residues in contact with ALA 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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146A ALA 3.1 13.1 + - - +
147A SER* 3.6 11.7 - - - +
148A LEU 3.2 0.2 - - - -
149A LEU* 1.3 75.8 - - - +
151A THR* 1.3 57.4 + - - +
154A PRO* 3.2 23.7 - - - +
164A VAL* 3.8 17.3 - - + +
166A ASN* 3.5 32.1 - - - +
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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 SER 3.2 10.9 + - - -
148A LEU* 2.9 12.2 + - + -
150A ALA* 1.3 80.6 - - - +
152A ILE* 1.3 68.7 + - + +
154A PRO* 3.6 10.4 - - - +
155A GLN* 3.4 36.2 - - - +
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Residues in contact with ILE 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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35A LEU* 3.7 32.7 - - + +
39A GLN* 3.8 32.8 - - + +
43A LEU* 4.4 9.4 - - + -
148A LEU* 2.9 56.1 + - + +
149A LEU* 4.0 11.2 - - + -
151A THR* 1.3 78.4 - - + +
153A ILE* 1.3 70.2 + - - +
155A GLN* 3.2 15.8 + - - +
156A TYR* 3.2 26.9 - - + -
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Residues in contact with ILE 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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32A LEU* 4.5 13.0 - - + -
35A LEU* 4.2 17.7 - - + -
121A ILE* 3.9 26.0 - - + -
124A MET* 4.6 10.5 - - + -
136A LEU* 4.7 3.8 - - + -
149A LEU* 3.0 33.4 + - + +
152A ILE* 1.3 75.7 - - - +
154A PRO* 1.3 68.0 - - + +
156A TYR* 3.1 3.1 + - - +
157A LEU* 2.8 42.0 + - + +
158A ASP 6.0 0.2 - - - +
162A TYR 3.6 24.5 - - - +
164A VAL* 3.7 13.7 - - + -
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Residues in contact with PRO 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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149A LEU 3.9 0.4 - - - +
150A ALA 3.2 26.2 - - - +
151A THR 3.6 8.7 - - - +
153A ILE* 1.3 98.9 - - + +
155A GLN* 1.3 58.9 + - + -
157A LEU 3.3 16.4 - - - +
158A ASP 5.5 0.7 - - - +
159A LYS* 2.8 46.6 + - + +
162A TYR 5.6 1.3 - - - +
164A VAL* 4.5 5.6 - - + +
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Residues in contact with GLN 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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34A ARG* 5.0 3.6 + - - -
39A GLN* 4.6 9.2 + - - -
151A THR* 3.4 33.5 + - - +
152A ILE* 3.2 21.4 + - - +
153A ILE 3.1 1.0 - - - -
154A PRO* 1.3 79.9 - - + +
156A TYR* 1.3 69.3 + - + +
159A LYS* 4.6 5.1 + - - +
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Residues in contact with TYR 156 (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 GLN* 4.8 1.6 + - - +
31A ALA* 3.4 38.5 - - + +
34A ARG* 3.4 36.0 + - + +
35A LEU* 3.8 35.0 - - + -
38A GLU* 2.6 35.8 + - - +
39A GLN* 3.1 37.9 + - + -
152A ILE* 3.2 26.1 + - + +
153A ILE 3.1 3.3 + - - +
155A GLN* 1.3 92.3 - - + +
157A LEU* 1.3 64.3 + - + +
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Residues in contact with LEU 157 (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 GLN* 3.2 37.0 - - - +
31A ALA* 3.6 15.9 - - + -
32A LEU* 3.7 32.8 - - + +
124A MET* 4.6 5.8 - - + -
128A ILE* 4.3 14.1 - - + -
153A ILE* 2.8 34.7 + - + +
154A PRO* 3.3 17.7 - - - +
156A TYR* 1.3 76.3 - - + +
158A ASP* 1.3 68.3 + - - +
159A LYS* 3.2 4.7 + - - +
162A TYR* 3.9 23.6 - - + -
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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