Contacts of the helix formed by residues 142 - 160 (chain I) in PDB entry 1A81
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 ALA 142 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138I LEU* 3.1 35.3 - - + +
139I GLN 2.6 10.9 + - - +
141I GLN* 1.3 79.7 - - - +
143I LEU* 1.3 62.0 + - - +
145I GLN* 3.0 21.7 + - - +
146I ALA* 3.4 6.4 + - - +
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Residues in contact with LEU 143 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129I ARG* 3.5 45.3 - - - +
132I VAL* 3.1 33.0 - - + -
133I LYS* 3.5 19.1 - - + +
138I LEU* 3.3 27.9 - - + +
139I GLN* 3.0 21.9 + - + +
140I GLY 5.2 1.3 - - - +
141I GLN 3.1 0.4 - - - -
142I ALA* 1.3 76.6 - - - +
144I GLU* 1.3 69.1 + - + +
145I GLN 3.1 1.0 + - - -
146I ALA* 3.5 7.3 + - - +
147I ILE* 3.0 23.3 + - + +
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Residues in contact with GLU 144 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140I GLY 3.4 13.7 - - - +
141I GLN* 3.3 25.1 - - + +
143I LEU* 1.3 75.1 - - + +
145I GLN* 1.3 65.3 + - - +
147I ILE* 2.8 18.2 - - - +
148I ILE* 2.6 34.8 - - + +
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Residues in contact with GLN 145 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141I GLN* 2.8 28.6 + - - +
142I ALA* 3.0 14.4 - - - +
144I GLU* 1.3 81.9 - - - +
146I ALA* 1.3 54.0 + - - +
147I ILE 2.6 16.3 + - - -
148I ILE* 2.8 25.6 + - + +
149I SER* 2.4 23.6 + - - +
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Residues in contact with ALA 146 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132I VAL* 4.4 4.5 - - + -
136I TRP* 3.5 31.4 - - + -
138I LEU* 4.3 10.5 - - + -
142I ALA 3.4 8.3 + - - +
143I LEU 3.7 8.7 - - - +
145I GLN* 1.3 76.9 - - - +
147I ILE* 1.3 50.1 + - - +
149I SER* 3.5 6.3 + - - -
150I GLN* 2.6 44.0 + - - +
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Residues in contact with ILE 147 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128I ILE* 4.5 11.7 - - + -
129I ARG* 4.3 26.2 - - + -
132I VAL* 4.1 26.0 - - + -
143I LEU* 3.0 24.9 - - + +
144I GLU* 2.8 31.4 - - - +
145I GLN 2.6 4.2 + - - -
146I ALA* 1.3 71.4 - - - +
148I ILE* 1.3 58.2 + - + +
149I SER 3.0 1.1 - - - -
150I GLN* 4.7 0.9 - - - -
151I LYS* 2.3 50.2 + - + +
154I LEU* 4.9 2.7 - - + -
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Residues in contact with ILE 148 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144I GLU* 2.6 32.1 - - + +
145I GLN* 2.8 31.4 + - + +
147I ILE* 1.3 75.5 - - + +
149I SER* 1.3 75.4 + - - +
151I LYS* 3.9 6.1 - - - +
152I PRO* 3.9 12.6 - - - +
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Residues in contact with SER 149 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145I GLN* 2.4 33.6 + - - +
146I ALA* 3.5 6.0 + - - -
148I ILE* 1.3 89.8 - - - +
150I GLN* 1.3 68.6 + - - +
152I PRO* 3.9 9.5 - - - +
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Residues in contact with GLN 150 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136I TRP* 3.4 24.2 - - + -
146I ALA* 2.6 23.8 + - - +
149I SER* 1.3 78.4 + - - +
151I LYS* 1.3 68.9 + - - +
152I PRO* 2.9 6.3 - - - +
153I GLN* 3.3 10.2 + - - +
154I LEU* 2.9 33.6 - - + +
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Residues in contact with LYS 151 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125I GLU* 3.9 26.1 + - - +
128I ILE* 6.3 4.9 - - + -
147I ILE* 2.3 37.4 + - + +
148I ILE* 3.9 7.4 - - - +
150I GLN* 1.3 66.9 - - - +
152I PRO* 1.3 65.8 - - + -
153I GLN 2.6 17.3 + - - -
154I LEU* 2.7 29.4 + - - +
155I GLU* 2.9 44.0 + - - -
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Residues in contact with PRO 152 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148I ILE 3.9 8.3 - - - +
149I SER 3.9 10.8 - - - +
150I GLN 3.3 6.7 - - - +
151I LYS* 1.3 96.1 - - + +
153I GLN* 1.3 59.4 + - + +
155I GLU* 3.0 23.4 - - - +
156I LYS* 4.9 1.7 + - - +
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Residues in contact with GLN 153 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150I GLN* 3.3 7.0 + - - +
151I LYS 2.6 5.7 + - - -
152I PRO* 1.3 75.0 - - + +
154I LEU* 1.3 78.6 + - + +
155I GLU 3.1 2.5 - - - -
156I LYS* 2.9 29.0 + - + +
157I LEU* 3.3 34.7 + - - +
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Residues in contact with LEU 154 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128I ILE* 5.3 13.0 - - + -
131I TYR* 6.0 1.6 - - + -
132I VAL* 4.7 11.4 - - + -
136I TRP* 4.0 17.5 - - + -
146I ALA 4.7 1.3 - - - +
147I ILE* 4.8 5.8 - - + +
150I GLN* 2.9 56.5 - - + +
151I LYS* 2.7 22.2 + - - +
153I GLN* 1.3 84.3 - - + +
155I GLU* 1.3 54.6 + - - +
157I LEU* 2.5 37.9 + - - +
158I ILE* 3.0 15.7 + - + +
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Residues in contact with GLU 155 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48I LEU* 6.3 0.4 - - - -
128I ILE* 5.6 3.8 - - + +
151I LYS* 2.9 49.1 + - - +
152I PRO* 3.0 28.2 - - - +
153I GLN 4.4 0.4 - - - +
154I LEU* 1.3 78.1 - - + +
156I LYS* 1.3 56.4 + - - +
157I LEU 2.7 10.9 + - - -
158I ILE* 3.3 5.5 + - - +
159I ALA* 3.0 26.2 + - - +
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Residues in contact with LYS 156 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48I LEU* 4.3 31.2 - - + +
152I PRO 4.9 1.7 + - - +
153I GLN* 2.9 26.2 + - + +
155I GLU* 1.3 75.2 - - - +
157I LEU* 1.3 60.1 + - + +
159I ALA* 4.4 4.7 - - - -
160I THR* 3.0 32.2 + - + +
235I ASP* 4.3 5.9 + - - -
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Residues in contact with LEU 157 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153I GLN* 3.3 33.5 + - - +
154I LEU* 2.5 19.7 + - - +
156I LYS* 1.3 76.2 - - + +
158I ILE* 1.3 75.1 + - + +
159I ALA 2.8 1.3 + - - -
160I THR* 2.7 24.1 + - - +
161I THR* 3.1 14.9 + - + +
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Residues in contact with ILE 158 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124I LYS* 4.7 11.2 - - + -
127I LEU* 3.6 30.7 - - + -
128I ILE* 3.1 42.2 - - + +
131I TYR* 4.7 22.2 - - + -
154I LEU* 3.0 13.8 + - + +
155I GLU* 4.1 7.0 - - - +
157I LEU* 1.3 84.2 - - + +
159I ALA* 1.3 60.4 + - - +
161I THR* 2.8 33.3 - - - +
162I ALA* 3.2 4.9 + - + +
238I TRP* 6.4 0.9 - - + -
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Residues in contact with ALA 159 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48I LEU* 4.5 17.7 - - + -
155I GLU 3.0 19.0 + - - +
156I LYS* 4.3 4.5 - - - +
157I LEU 2.8 1.0 + - - -
158I ILE* 1.3 78.6 - - - +
160I THR* 1.3 56.4 + - + +
161I THR 2.5 17.5 + - - -
162I ALA* 3.2 14.6 + - - +
163I HIS* 4.7 0.9 + - - -
236I THR* 4.1 22.6 - - + +
238I TRP* 5.3 18.4 - - + +
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Residues in contact with THR 160 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48I LEU* 5.6 3.6 - - + -
156I LYS* 3.0 24.7 + - + +
157I LEU* 2.7 23.0 + - - +
159I ALA* 1.3 76.8 - - + +
161I THR* 1.3 65.4 + - - +
163I HIS* 3.0 18.0 - - - -
200I ASN* 5.7 0.9 - - - +
220I LYS* 6.2 1.6 - - - +
235I ASP* 5.7 3.8 - - + +
236I THR* 4.0 19.3 - - + +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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