Contacts of the helix formed by residues 126 - 144 (chain B) in PDB entry 1W98
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 GLN 126 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119B LEU* 4.4 7.4 - - - +
124B LEU 4.9 2.1 + - - +
125B LEU* 1.3 78.7 - - - +
127B PRO* 1.3 76.2 - - + +
128B LYS* 3.1 39.2 + - + +
129B MET* 3.1 45.2 + - + +
130B ARG 3.7 1.9 + - - -
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Residues in contact with PRO 127 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119B LEU* 3.9 20.8 - - + -
125B LEU 4.9 0.9 - - - +
126B GLN* 1.3 85.8 - - + +
128B LYS* 1.3 60.8 + - - +
130B ARG* 3.1 14.6 + - - +
131B ALA* 3.2 12.1 + - - +
274B VAL* 4.0 19.3 - - + +
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Residues in contact with LYS 128 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126B GLN* 3.1 27.8 + - + +
127B PRO* 1.3 75.2 - - - +
129B MET* 1.3 63.1 + - + +
131B ALA* 3.8 9.0 - - + +
132B ILE* 3.0 46.5 + - + +
352B LEU* 6.4 0.7 - - + -
355B LEU* 5.9 3.1 - - + -
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Residues in contact with MET 129 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119B LEU* 6.5 0.2 - - + -
124B LEU 3.7 15.7 - - - +
125B LEU* 3.7 24.0 - - + -
126B GLN* 3.1 50.7 + - + +
128B LYS* 1.3 78.8 - - + +
130B ARG* 1.3 58.7 + - - +
132B ILE* 3.3 10.4 + - + +
133B LEU* 2.8 31.8 + - - +
170B LYS* 4.2 28.0 - - + -
173B LEU* 3.9 17.0 - - + +
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Residues in contact with ARG 130 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118B PHE* 3.8 10.1 - - - -
119B LEU* 4.2 14.5 - - + +
126B GLN 3.7 1.6 + - - -
127B PRO 3.1 10.6 + - - +
129B MET* 1.3 77.0 - - - +
131B ALA* 1.3 57.5 + - - +
133B LEU* 3.5 5.9 + - - +
134B LEU* 2.9 42.5 + - + +
155B GLN* 4.4 3.2 - - - +
158B PHE* 3.9 20.9 - - + -
159B ASP* 2.8 39.6 + - - -
173B LEU* 5.0 2.1 - - - +
271B VAL* 2.7 30.5 + - - +
272B LEU 3.5 9.9 + - - -
274B VAL* 3.2 47.7 - - + +
276B CYS* 4.4 6.5 - - - -
277B LEU* 4.3 10.9 - - - +
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Residues in contact with ALA 131 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127B PRO 3.2 10.0 + - - +
128B LYS* 4.0 8.1 - - + +
130B ARG* 1.3 76.0 - - - +
132B ILE* 1.3 60.6 + - - +
134B LEU* 4.5 1.3 - - - +
135B ASP* 2.8 32.1 + - - +
272B LEU* 3.1 38.6 - - + +
352B LEU* 3.9 7.0 - - + +
355B LEU* 3.8 22.0 - - + -
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Residues in contact with ILE 132 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128B LYS* 3.0 35.7 + - + +
129B MET* 3.6 8.7 - - + +
131B ALA* 1.3 75.5 - - - +
133B LEU* 1.3 65.4 + - - +
135B ASP* 3.7 2.8 - - - +
136B TRP* 3.0 26.0 + - + +
352B LEU* 4.1 27.3 - - + +
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Residues in contact with LEU 133 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129B MET 2.8 17.6 + - - +
130B ARG* 3.7 4.9 - - - +
132B ILE* 1.3 80.0 - - - +
134B LEU* 1.3 64.3 + - + +
136B TRP* 3.4 21.1 + - + +
137B LEU* 3.0 28.1 + - + +
158B PHE* 3.5 46.0 - - + -
173B LEU* 3.5 39.0 - - + +
174B GLN* 4.0 10.5 - - + +
177B GLY* 4.1 10.3 - - - -
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Residues in contact with LEU 134 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130B ARG* 2.9 64.6 + - + +
131B ALA 4.1 3.1 - - - +
133B LEU* 1.3 76.3 - - + +
135B ASP* 1.3 56.0 + - - +
137B LEU* 3.3 16.7 + - + -
138B MET* 3.1 31.9 + - - +
151B PHE* 3.4 10.7 - - + -
155B GLN* 4.0 37.0 - - + -
158B PHE* 4.1 20.6 - - + -
159B ASP* 4.7 0.4 - - - +
271B VAL* 3.6 12.1 - - + +
272B LEU* 4.2 11.0 - - + -
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Residues in contact with ASP 135 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131B ALA 2.8 22.9 + - - +
132B ILE 3.7 4.2 - - - +
134B LEU* 1.3 68.7 - - - +
136B TRP* 1.3 66.0 + - - +
138B MET* 3.3 7.6 + - - +
139B GLU* 3.2 17.2 + - - +
272B LEU* 4.1 12.3 - - + +
348B HIS* 2.8 40.7 + - - -
349B ARG 3.8 6.9 - - - +
350B ASP* 5.4 0.3 - - - -
351B SER* 4.3 12.1 + - - -
352B LEU* 3.5 34.5 + - + +
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Residues in contact with TRP 136 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132B ILE* 3.0 19.3 + - + +
133B LEU* 3.6 20.4 - - + +
135B ASP* 1.3 76.6 + - - +
137B LEU* 1.3 95.1 - - + +
139B GLU* 3.1 16.8 + - + +
140B VAL* 2.9 38.2 + - + +
174B GLN* 3.5 39.0 + - + -
178B ILE* 3.9 28.3 - - + -
201B VAL* 3.8 23.5 + - - +
202B THR* 4.4 2.9 - - + -
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Residues in contact with LEU 137 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133B LEU* 3.0 22.6 + - + +
134B LEU* 3.3 25.5 + - + +
136B TRP* 1.3 99.2 - - + +
138B MET* 1.3 57.5 + - - +
140B VAL* 3.4 4.7 + - + +
141B CYS* 2.9 33.1 + - - -
151B PHE* 4.0 12.6 - - + -
154B ALA* 4.7 18.2 - - + +
158B PHE* 5.7 1.1 - - + -
177B GLY* 3.6 36.8 - - - +
178B ILE* 4.0 3.4 - - + +
180B SER* 5.7 0.2 - - - -
181B LEU* 3.8 24.4 - - + +
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Residues in contact with MET 138 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134B LEU 3.1 17.3 + - - +
135B ASP* 3.5 12.8 - - - +
136B TRP 3.2 0.4 - - - -
137B LEU* 1.3 75.1 - - - +
139B GLU* 1.3 58.0 + - - +
141B CYS* 3.4 3.8 + - - +
142B GLU* 3.0 26.7 + - - +
151B PHE* 3.5 33.4 - - + -
268B ASP* 3.5 39.9 - - + +
272B LEU* 4.3 12.3 - - - -
346B GLN* 3.5 20.4 - - - +
347B THR 3.4 22.0 - - - +
348B HIS* 4.1 15.3 - - + +
349B ARG 5.3 0.4 - - - +
351B SER* 4.8 10.3 - - - +
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Residues in contact with GLU 139 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135B ASP* 3.2 5.5 + - - +
136B TRP* 3.1 19.2 + - + +
138B MET* 1.3 77.5 - - - +
140B VAL* 1.3 65.4 + - - +
142B GLU* 3.2 4.8 + - + +
143B VAL* 3.0 37.5 + - + +
348B HIS* 3.7 44.9 + - + +
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Residues in contact with VAL 140 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136B TRP* 2.9 53.1 + - + +
137B LEU* 3.9 11.7 - - + -
139B GLU* 1.3 72.7 - - - +
141B CYS* 1.3 63.9 + - - +
143B VAL* 3.2 7.6 + - - -
144B TYR* 3.0 38.9 + - + -
146B LEU* 5.0 2.2 - - + -
178B ILE* 4.3 1.6 - - + -
181B LEU* 3.5 22.4 - - + -
198B PHE* 5.3 2.9 - - + -
201B VAL* 4.0 26.7 - - + -
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Residues in contact with CYS 141 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137B LEU 2.9 22.2 + - - -
138B MET 3.4 9.9 - - - +
139B GLU 3.3 0.2 - - - -
140B VAL* 1.3 70.5 - - - +
142B GLU* 1.3 58.1 + - - +
144B TYR 3.4 0.3 + - - -
145B LYS* 2.8 7.4 + - - -
146B LEU* 2.8 48.0 + - + +
151B PHE* 3.8 26.2 - - - -
181B LEU* 3.7 29.4 - - - -
346B GLN* 3.7 20.9 - - + -
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Residues in contact with GLU 142 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138B MET 3.0 13.3 + - - +
139B GLU* 3.7 9.6 - - + +
140B VAL 3.2 0.4 - - - -
141B CYS* 1.3 74.8 - - - +
143B VAL* 1.3 66.2 + - + +
145B LYS* 3.0 20.6 + - - +
332B LYS* 3.1 28.2 + - - +
334B PHE* 4.3 12.8 - - + -
345B ILE* 5.2 0.5 - - - +
346B GLN 3.2 20.4 + - - +
347B THR* 3.7 9.8 - - - +
348B HIS* 2.7 39.8 + - - +
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Residues in contact with VAL 143 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139B GLU* 3.0 28.3 + - + +
140B VAL* 3.5 10.8 - - - +
142B GLU* 1.3 77.7 - - + +
144B TYR* 1.3 79.8 - - + +
145B LYS* 3.7 12.3 + - - +
201B VAL* 5.6 3.8 - - + -
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Residues in contact with TYR 144 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140B VAL* 3.0 33.9 + - + +
143B VAL* 1.3 90.3 - - + +
145B LYS* 1.3 71.2 + - - +
146B LEU* 3.1 26.4 + - + +
193B PRO* 3.9 18.2 - - + +
197B GLN* 3.5 51.0 + - + +
198B PHE* 6.3 1.3 - + - -
200B TYR* 3.9 19.4 - - - -
201B VAL* 4.0 26.7 - - + +
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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
------------------------------------------------------------
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