Contacts of the helix formed by residues 125 - 141 (chain D) in PDB entry 2O1S
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 THR 125 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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375C THR* 3.4 23.6 - - + -
405C HIS* 4.7 2.6 - - + -
406C ASP* 3.3 28.7 + - - +
77D ASP* 3.4 1.2 + - - -
118D LEU* 3.5 25.1 - - + -
119D SER 5.6 0.2 - - - +
120D VAL* 4.7 9.0 - - + -
122D HIS 4.2 7.3 + - - -
123D SER 3.2 9.4 + - - -
124D SER* 1.3 78.1 - - - +
126D SER* 1.3 67.2 + - - +
127D ILE 3.5 0.4 - - - -
128D SER* 3.2 5.2 + - - -
129D ALA* 3.2 15.6 + - - +
159D MSE 4.1 6.0 - - - -
398D ARG* 4.1 8.7 + - - -
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Residues in contact with SER 126 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75D ILE* 3.7 25.4 + - - +
77D ASP* 3.3 32.6 + - - +
118D LEU* 4.1 2.6 - - - +
125D THR* 1.3 77.6 - - - +
127D ILE* 1.3 58.3 + - - +
129D ALA* 4.1 1.2 - - - +
130D GLY* 2.7 29.1 + - - -
148D CYS* 3.0 27.6 - - - +
149D VAL 3.9 2.3 + - - -
150D ILE* 3.5 11.0 - - - -
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Residues in contact with ILE 127 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124D SER 4.7 3.1 + - - +
125D THR 3.5 0.6 - - - -
126D SER* 1.3 74.9 - - - +
128D SER* 1.3 62.8 + - - +
130D GLY* 3.4 0.3 - - - -
131D ILE* 2.9 39.5 + - + +
148D CYS* 4.4 7.6 - - + -
150D ILE* 4.4 15.9 - - + +
155D ILE* 4.3 16.6 - - + -
160D ALA* 4.4 11.2 - - + +
163D ALA* 3.5 27.4 - - + -
164D MSE 3.8 25.8 - - + +
174D MSE 4.3 8.0 - - + +
176D VAL* 4.1 35.0 - - + -
248D PHE* 5.2 2.0 - - + -
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Residues in contact with SER 128 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372C HIS* 2.9 41.6 - - - +
375C THR* 3.3 28.4 - - - -
376C PHE* 3.9 6.4 - - - -
124D SER 4.8 2.2 + - - -
125D THR* 3.2 7.6 + - - -
127D ILE* 1.3 78.3 - - - +
129D ALA* 1.3 68.1 + - - +
130D GLY 3.2 0.2 + - - -
131D ILE* 3.2 12.8 + - - +
132D GLY 3.4 8.0 + - - -
159D MSE 3.9 11.7 + - - +
163D ALA* 3.7 6.3 - - - +
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Residues in contact with ALA 129 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375C THR* 3.4 20.9 - - + +
378C ALA* 5.1 0.7 - - + -
379C GLY* 3.4 11.7 - - - +
382C ILE* 5.0 0.9 - - + -
75D ILE* 5.5 0.4 - - + -
118D LEU* 3.7 40.8 - - + -
125D THR 3.2 4.4 + - - +
128D SER* 1.3 78.6 - - - +
130D GLY* 1.3 63.1 + - - +
132D GLY 3.2 1.4 + - - -
133D ILE* 2.9 37.3 + - + +
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Residues in contact with GLY 130 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75D ILE* 4.5 6.7 - - - +
126D SER 2.7 21.3 + - - -
127D ILE 3.4 2.5 - - - -
128D SER 3.0 0.4 - - - -
129D ALA* 1.3 79.3 - - - +
131D ILE* 1.3 56.1 + - - +
133D ILE* 3.4 1.4 + - - +
134D ALA* 2.9 26.5 + - - +
146D THR* 3.5 12.2 - - - +
148D CYS* 3.7 16.6 - - - -
174D MSE 3.7 6.5 - - - -
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Residues in contact with ILE 131 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372C HIS* 3.7 7.4 - - - +
376C PHE* 3.3 24.9 - - + -
127D ILE* 2.9 24.8 + - + +
128D SER 3.2 5.3 + - - +
130D GLY* 1.3 72.7 - - - +
132D GLY* 1.3 59.4 + - - +
134D ALA* 3.4 7.9 - - - +
135D VAL* 2.6 39.8 + - - +
163D ALA 4.6 3.1 - - - +
166D HIS* 3.0 37.2 - - + +
167D ALA* 4.3 12.3 - - + +
170D ILE* 3.7 13.7 - - + -
172D PRO* 4.5 6.7 - - + -
174D MSE 3.5 22.2 - - + -
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Residues in contact with GLY 132 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376C PHE* 3.4 36.3 - - - -
379C GLY 3.6 6.7 - - - -
380C LEU* 3.3 15.7 - - - +
128D SER 3.4 2.2 + - - -
129D ALA 3.2 6.9 + - - -
131D ILE* 1.3 82.5 - - - +
133D ILE* 1.3 56.2 + - - +
136D ALA* 3.0 24.6 + - - +
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Residues in contact with ILE 133 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379C GLY* 3.5 18.6 - - - +
382C ILE* 4.1 19.1 - - + -
383C GLY* 4.9 4.9 - - - +
73D GLN* 3.6 35.2 - - + +
75D ILE* 4.1 15.3 - - + -
117D VAL* 3.4 28.7 - - + -
118D LEU* 5.4 0.9 - - + -
129D ALA* 2.9 25.1 + - + +
130D GLY* 3.6 4.5 - - - +
132D GLY* 1.3 75.5 - - - +
134D ALA* 1.3 59.4 + - - +
136D ALA* 3.3 6.4 + - - +
137D ALA* 2.9 26.3 + - - +
144D ARG* 5.5 2.3 - - - -
146D THR* 3.9 7.9 - - + +
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Residues in contact with ALA 134 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130D GLY 2.9 17.5 + - - +
131D ILE* 3.0 9.2 + - - +
133D ILE* 1.3 76.9 - - - +
135D VAL* 1.3 64.0 + - - +
137D ALA* 3.3 5.0 + - - +
138D GLU* 3.0 22.0 + - - +
146D THR* 3.5 18.6 - - - +
172D PRO* 4.1 15.1 - - + +
173D ASP* 3.8 23.2 + - - +
174D MSE 4.1 4.7 - - + -
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Residues in contact with VAL 135 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340C MSE 5.6 0.4 - - - -
364C PHE* 3.7 28.3 - - + -
376C PHE* 3.9 11.0 - - + -
380C LEU* 4.2 11.2 - - + -
131D ILE 2.6 24.3 + - - +
132D GLY 3.8 4.5 - - - +
134D ALA* 1.3 72.3 - - - +
136D ALA* 1.3 63.3 + - - +
138D GLU* 3.2 9.5 + - + +
139D LYS* 3.2 36.6 + - + +
170D ILE* 3.8 28.3 - - + -
172D PRO* 4.4 8.3 - - + -
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Residues in contact with ALA 136 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
380C LEU* 4.4 4.9 - - + +
383C GLY* 3.7 30.9 - - - +
385C TYR* 3.7 30.3 - - + -
132D GLY 3.0 18.0 + - - +
133D ILE 3.4 6.3 - - - +
134D ALA 3.2 0.2 - - - -
135D VAL* 1.3 79.1 - - - +
137D ALA* 1.3 60.9 + - - +
139D LYS* 3.4 2.6 + - - +
140D GLU* 3.0 21.9 + - - +
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Residues in contact with ALA 137 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133D ILE 2.9 14.4 + - - +
134D ALA* 3.3 12.7 + - - +
136D ALA* 1.3 74.8 - - - +
138D GLU* 1.3 63.5 + - - +
140D GLU* 3.1 26.7 + - - +
141D GLY* 3.2 6.6 + - - -
142D LYS 4.6 1.9 + - - -
143D ASN* 4.8 4.3 + - - -
144D ARG* 3.3 42.9 + - + +
146D THR* 4.6 3.6 - - - +
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Residues in contact with GLU 138 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134D ALA 3.0 12.2 + - - +
135D VAL* 3.2 15.7 - - + +
137D ALA* 1.3 79.3 - - - +
139D LYS* 1.3 74.3 + - + +
140D GLU 3.3 0.7 + - - -
141D GLY* 3.4 10.7 + - - -
172D PRO* 6.5 0.9 - - + -
173D ASP* 5.5 7.3 - - + +
273D LYS* 5.5 5.2 + - - -
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Residues in contact with LYS 139 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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337C ASN* 6.0 0.8 + - - +
340C MSE 3.7 25.9 - - + +
361C ASP* 2.7 39.4 + - - +
362C ARG* 5.0 0.6 - - - +
364C PHE* 4.4 8.6 - - - -
385C TYR* 3.1 31.6 + - + +
135D VAL* 3.2 21.1 + - + +
136D ALA* 3.9 2.2 - - - +
138D GLU* 1.3 85.2 - - + +
140D GLU* 1.3 61.0 + - - +
141D GLY* 4.6 0.3 - - - -
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Residues in contact with GLU 140 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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383C GLY 6.1 0.9 - - - -
385C TYR* 4.2 5.8 - - + +
71D PHE* 4.4 0.7 - - - -
136D ALA 3.0 13.0 + - - +
137D ALA* 3.1 13.8 + - - +
139D LYS* 1.3 79.5 - - - +
141D GLY* 1.3 55.8 + - - +
142D LYS* 3.1 38.1 + - + +
144D ARG* 2.8 57.9 + - - +
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Residues in contact with GLY 141 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137D ALA 3.2 7.0 + - - -
138D GLU 3.4 9.8 + - - -
139D LYS 3.4 0.4 - - - -
140D GLU* 1.3 77.1 - - - +
142D LYS* 1.3 57.9 + - - +
143D ASN* 3.1 11.8 + - - +
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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