Contacts of the helix formed by residues 140 - 153 (chain D) in PDB entry 2W8I
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 140 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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84D GLU* 3.7 31.9 + - + +
85D TYR 4.0 12.1 - - - +
86D ARG* 3.4 30.5 - - - +
87D ILE* 4.3 0.2 - - - -
139D LYS* 1.3 74.3 - - - +
141D VAL* 1.3 69.4 + - - +
142D SER* 2.9 7.7 + - - -
143D GLN* 2.9 33.7 + - - +
144D VAL* 2.8 24.0 + - - +
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Residues in contact with VAL 141 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119A TRP* 6.0 4.7 - - + -
121A ASN* 3.9 24.0 - - + +
85D TYR* 4.8 4.8 + - + +
87D ILE* 4.3 6.8 - - + +
140D THR* 1.3 73.6 - - - +
142D SER* 1.3 53.5 + - - +
144D VAL* 3.5 7.9 + - - +
145D ARG* 2.7 36.3 + - - +
163D VAL* 3.6 30.6 - - + +
164D SER* 3.9 8.7 - - - -
165D ILE* 3.6 34.5 - - + -
189D ASN* 6.5 0.9 - - + -
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Residues in contact with SER 142 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A ASN* 4.0 16.1 + - - +
122A SER* 5.6 0.9 + - - -
123A ASP* 5.5 0.9 - - - -
133A LYS* 4.0 12.1 + - - -
140D THR* 3.0 7.0 + - - -
141D VAL* 1.3 78.4 - - - +
143D GLN* 1.3 66.4 + - - +
145D ARG* 2.9 33.7 + - - +
146D GLN* 2.9 36.0 + - - +
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Residues in contact with GLN 143 (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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86D ARG* 3.4 22.5 + - - +
139D LYS* 3.4 27.1 - - + +
140D THR* 2.9 36.9 + - - +
142D SER* 1.3 78.6 - - - +
144D VAL* 1.3 63.4 + - - +
146D GLN* 3.2 12.4 + - - +
147D ASP* 2.9 23.8 + - - +
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Residues in contact with VAL 144 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87D ILE* 3.4 31.0 - - + -
93D LEU* 4.5 10.5 - - + -
134D VAL* 5.3 2.7 - - + -
135D GLN 5.0 0.9 - - - +
136D VAL* 3.8 23.3 - - + -
139D LYS* 4.0 13.7 - - + +
140D THR 2.8 14.2 + - - +
141D VAL* 3.5 9.0 - - - +
143D GLN* 1.3 73.6 - - - +
145D ARG* 1.3 63.7 + - - +
147D ASP* 3.1 7.9 + - - +
148D ILE* 2.9 44.6 + - + +
163D VAL* 4.3 13.7 - - + -
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Residues in contact with ARG 145 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A ASN* 3.2 26.0 + - - +
127A PHE* 4.1 23.1 - - - +
133A LYS* 3.5 24.2 - - - +
141D VAL 2.7 22.1 + - - +
142D SER* 2.9 35.7 + - - +
144D VAL* 1.3 73.6 - - - +
146D GLN* 1.3 68.1 + - + +
148D ILE* 3.4 2.1 + - - +
149D THR* 2.8 30.0 + - - +
161D VAL* 3.0 32.0 - - - +
162D ASP* 2.6 37.8 + - - +
163D VAL* 4.0 23.2 + - + -
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Residues in contact with GLN 146 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133A LYS* 5.2 8.3 + - - +
142D SER* 2.9 25.9 + - - +
143D GLN* 3.7 11.2 + - - +
145D ARG* 1.3 82.4 - - + +
147D ASP* 1.3 64.4 + - - +
149D THR* 3.2 6.9 + - - -
150D SER* 3.0 27.2 + - - -
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Residues in contact with ASP 147 (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 VAL* 3.6 21.7 - - + +
135D GLN* 3.8 1.0 + - - +
139D LYS* 2.9 27.9 + - - +
143D GLN 2.9 14.2 + - - +
144D VAL* 3.3 12.8 - - - +
146D GLN* 1.3 78.9 - - - +
148D ILE* 1.3 62.3 + - - +
150D SER* 3.3 7.8 + - - -
151D ARG* 3.2 37.6 + - - +
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Residues in contact with ILE 148 (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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95D VAL* 4.0 33.9 - - + -
126D ILE* 4.5 12.8 - - + -
128D TYR* 4.6 7.4 - - + -
131D ILE* 4.0 22.3 - - + +
134D VAL* 4.4 12.6 - - + -
144D VAL* 2.9 39.9 + - + +
145D ARG 4.0 3.4 - - - +
147D ASP* 1.3 70.3 - - - +
149D THR* 1.3 62.4 + - - +
151D ARG* 3.6 0.9 + - - +
152D LEU* 2.8 52.8 + - + +
161D VAL* 4.2 12.1 - - + -
163D VAL* 4.2 4.5 - - + -
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Residues in contact with THR 149 (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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145D ARG* 2.8 25.3 + - - +
146D GLN* 3.2 7.7 + - - -
148D ILE* 1.3 76.9 - - - +
150D SER* 1.3 65.7 + - - +
152D LEU* 2.9 17.0 + - - +
153D THR* 3.1 15.2 + - - +
159D PRO* 3.5 33.4 - - + +
161D VAL* 3.6 23.6 + - + +
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Residues in contact with SER 150 (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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146D GLN 3.0 14.4 + - - -
147D ASP* 3.3 12.0 + - - -
149D THR* 1.3 77.9 - - - +
151D ARG* 1.3 80.7 + - - +
153D THR* 3.1 25.2 + - - -
154D THR* 4.4 1.9 + - - +
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Residues in contact with ARG 151 (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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131D ILE* 2.7 56.9 + - + +
133D LYS 3.1 25.9 + - - +
134D VAL* 3.4 28.1 - - - +
135D GLN 4.7 1.0 - - - +
147D ASP* 3.2 34.4 + - - +
149D THR 3.2 0.6 - - - -
150D SER* 1.3 87.7 + - - +
152D LEU* 1.3 57.8 + - - +
153D THR 3.0 4.7 + - - -
154D THR* 3.2 24.0 - - - +
155D TYR* 4.1 1.0 - - - -
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Residues in contact with LEU 152 (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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97D VAL* 4.8 7.2 - - + -
103D LEU* 5.0 3.1 - - + -
128D TYR* 4.3 16.6 - - + -
129D PRO 4.6 2.2 - - - +
130D TYR* 4.5 19.3 - - + -
131D ILE* 3.8 17.0 - - + -
148D ILE* 2.8 39.6 + - + +
149D THR* 2.9 7.7 + - - +
151D ARG* 1.3 76.6 - - - +
153D THR* 1.3 58.0 + - - +
154D THR 3.4 0.2 - - - -
155D TYR* 3.0 18.7 + - + -
156D ILE* 3.2 34.3 + - + +
159D PRO* 3.9 6.5 - - + -
161D VAL* 4.0 17.7 - - + -
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Residues in contact with THR 153 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149D THR* 3.1 11.9 + - - +
150D SER* 3.1 23.0 + - - -
151D ARG 3.0 0.6 - - - -
152D LEU* 1.3 73.9 - - - +
154D THR* 1.3 66.8 + - - +
155D TYR 3.0 2.7 + - - -
156D ILE 3.4 14.5 + - - +
157D GLU* 5.1 1.5 - - - -
158D SER 5.5 1.8 - - - +
159D PRO* 3.7 19.9 - - + +
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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