Contacts of the helix formed by residues 128 - 141 (chain B) in PDB entry 4KSL
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 TYR 128 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126B ASP* 2.7 19.9 + - - +
127B ASN* 1.3 72.7 - - - +
129B ALA* 1.3 62.6 + - - -
130B ALA 3.3 2.2 - - - -
131B LEU* 3.0 19.3 + - + +
132B ARG* 2.9 19.4 + - - +
173B LEU 5.3 1.6 - - - -
226B TYR* 3.4 46.6 - + + +
229B TYR* 3.5 45.5 - + + -
230B GLU* 3.2 23.0 + - - +
233B LYS* 4.1 16.8 + - + -
280B VAL* 4.1 3.1 - - + -
281B GLY* 3.3 38.9 - - - -
282B HIS* 4.6 6.9 - + - -
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Residues in contact with ALA 129 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123B VAL* 3.9 2.5 - - + +
124B ARG 3.4 23.1 - - - +
126B ASP* 3.0 3.4 + - - -
127B ASN 3.2 2.8 - - - -
128B TYR* 1.3 75.6 - - - +
130B ALA* 1.3 57.6 + - - +
132B ARG* 3.6 6.6 - - - +
133B ALA* 2.9 31.4 + - - +
339B HIS* 3.4 22.2 - - + +
340B TYR* 4.7 3.7 - - - +
76C GLY* 3.2 27.1 - - - +
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Residues in contact with ALA 130 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127B ASN 4.9 1.7 + - - +
128B TYR 3.3 1.0 - - - -
129B ALA* 1.3 78.0 - - - +
131B LEU* 1.3 58.8 + - - +
133B ALA* 3.9 1.7 - - - +
134B THR* 3.0 36.0 + - - -
286B LEU* 4.0 19.5 - - + +
291B MET* 3.9 20.2 - - + -
294B LEU* 4.4 1.3 - - + -
332B LEU* 5.5 0.2 - - - -
340B TYR* 3.8 33.7 - - + -
75C GLY 5.1 3.8 - - - +
76C GLY* 4.8 2.2 - - - -
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Residues in contact with LEU 131 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128B TYR* 3.0 16.4 + - + +
130B ALA* 1.3 73.6 - - + +
132B ARG* 1.3 62.1 + - - +
134B THR* 4.8 0.2 - - - -
135B LEU* 2.9 36.0 + - + +
229B TYR* 3.9 43.5 - - + +
232B VAL* 3.9 10.8 - - + -
233B LYS* 3.9 8.3 - - + -
236B MET* 3.7 19.3 - - + -
280B VAL* 4.6 8.7 - - + -
286B LEU* 3.6 28.5 - - + -
294B LEU* 3.6 27.8 - - + -
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Residues in contact with ARG 132 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81B SER* 3.3 30.6 - - - -
82B VAL* 4.2 10.3 - - + -
123B VAL* 3.7 13.2 - - + -
124B ARG* 3.2 24.2 + - - +
126B ASP* 2.5 46.9 + - - -
128B TYR* 2.9 8.9 + - - +
129B ALA* 3.6 10.6 - - - +
130B ALA 3.3 0.2 - - - -
131B LEU* 1.3 77.2 - - - +
133B ALA* 1.3 57.5 + - - +
136B PHE* 2.9 34.1 + - - +
219B PHE* 4.1 3.6 - - + -
222B GLU* 3.6 12.5 + - - -
225B GLU* 2.4 28.2 + - - +
226B TYR* 3.9 2.6 - - - -
229B TYR* 3.1 34.2 - - - +
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Residues in contact with ALA 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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82B VAL* 5.8 0.4 - - - -
123B VAL* 4.1 16.1 - - + +
129B ALA 2.9 16.6 + - - +
130B ALA 3.9 2.9 - - - +
132B ARG* 1.3 78.9 - - - +
134B THR* 1.3 63.5 + - - +
136B PHE* 3.8 3.1 - - - +
137B GLN* 2.9 26.2 + - - +
332B LEU* 3.8 12.1 - - + -
340B TYR* 4.2 14.8 - - + -
342B ILE* 3.8 26.0 - - + +
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Residues in contact with THR 134 (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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130B ALA 3.0 18.2 + - - -
131B LEU* 4.2 1.3 - - - -
133B ALA* 1.3 76.5 - - - +
135B LEU* 1.3 60.0 + - - +
137B GLN* 3.7 3.2 - - - +
138B ALA* 2.9 28.8 + - + +
291B MET* 4.8 0.5 - - - +
294B LEU* 3.7 14.6 - - + +
298B VAL* 4.3 18.6 - - + -
300B HIS* 5.1 2.5 - - + -
302B ILE* 3.5 38.1 - - + +
330B VAL* 4.2 10.2 - - + +
332B LEU* 3.6 19.2 - - - +
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Residues in contact with LEU 135 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131B LEU 2.9 19.5 + - - +
132B ARG 4.3 0.9 - - - +
134B THR* 1.3 75.6 - - - +
136B PHE* 1.3 60.0 + - - +
138B ALA* 3.7 2.9 - - + +
139B MET* 2.9 44.9 + - - +
195B LEU* 4.4 6.5 - - + -
199B TRP* 4.0 27.1 - - + -
219B PHE* 4.2 3.8 - - + -
228B LEU* 3.7 39.5 - - + -
229B TYR* 4.1 14.4 - - + -
232B VAL* 4.1 27.8 - - + -
298B VAL* 4.6 11.4 - - + -
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Residues in contact with PHE 136 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80B LEU* 6.0 0.4 - - + -
82B VAL* 3.7 29.8 - - + -
121B ARG* 3.4 23.1 - - - -
132B ARG 2.9 20.5 + - - +
133B ALA* 3.8 4.0 - - - +
135B LEU* 1.3 76.0 - - - +
137B GLN* 1.3 68.7 + - - +
140B SER* 2.8 54.8 + - - -
212B GLN 5.5 0.7 - - - -
215B CYS* 4.2 10.9 - - + -
216B ASP* 3.3 28.3 - - - -
219B PHE* 3.4 45.4 - + + -
342B ILE* 5.0 10.3 - - + -
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Residues in contact with GLN 137 (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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133B ALA 2.9 17.4 + - - +
134B THR* 3.7 1.3 - - - +
136B PHE* 1.3 82.3 - - - +
138B ALA* 1.3 62.3 + - - +
140B SER* 3.0 22.3 + - - -
141B GLN* 3.4 24.1 + - - +
330B VAL* 3.6 32.3 - - + +
331B THR* 3.3 17.1 - - - +
332B LEU* 4.8 1.3 - - + -
342B ILE* 3.1 43.5 - - + +
343B PRO 4.1 6.3 + - - +
344B VAL* 5.9 0.8 - - - +
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Residues in contact with ALA 138 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134B THR* 2.9 19.8 + - + +
135B LEU* 3.7 7.9 - - + +
137B GLN* 1.3 79.9 - - - +
139B MET* 1.3 60.6 + - - +
141B GLN* 3.8 2.3 + - - +
142B ALA* 3.5 20.3 + - - +
199B TRP* 3.9 12.8 - - + -
298B VAL* 5.9 2.0 - - + -
300B HIS* 3.4 38.8 + - + +
330B VAL* 3.7 8.7 - - + +
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Residues in contact with MET 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 LEU* 2.9 44.2 + - + +
138B ALA* 1.3 74.2 - - - +
140B SER* 1.3 64.5 + - - +
141B GLN 3.2 0.4 - - - -
142B ALA* 3.3 19.2 + - - +
195B LEU* 4.4 8.3 - - + -
198B LYS* 3.9 6.1 - - + -
199B TRP* 3.6 57.0 - - + +
202B LEU* 3.6 23.2 - - + +
211B ARG* 4.1 4.2 - - - -
215B CYS* 4.0 7.6 - - - -
218B LEU* 3.6 26.9 - - + -
219B PHE* 4.5 4.3 - - - -
228B LEU* 4.3 9.2 - - + -
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Residues in contact with SER 140 (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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136B PHE* 2.8 39.9 + - - -
137B GLN* 3.0 20.8 + - - -
139B MET* 1.3 78.3 - - - +
141B GLN* 1.3 53.1 + - - +
211B ARG* 2.6 32.1 + - - +
212B GLN* 3.9 15.9 + - - +
215B CYS* 3.7 23.8 - - - -
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Residues in contact with GLN 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 GLN* 3.4 22.9 + - - +
138B ALA 4.1 3.1 - - - +
139B MET 3.2 0.2 - - - -
140B SER* 1.3 81.1 + - - +
142B ALA* 1.3 58.7 + - - +
143B VAL* 3.2 8.8 + - + +
211B ARG* 3.1 24.9 + - - +
212B GLN* 6.2 0.2 - - - +
329B VAL 5.2 6.1 - - - +
330B VAL* 6.2 0.2 - - - +
345B ARG* 4.2 21.6 + - - +
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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