Contacts of the helix formed by residues 135 - 151 (chain A) in PDB entry 1YK1
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 135 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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115A LEU* 3.9 17.7 - - - +
117A ALA* 6.5 0.2 - - - -
131A ARG* 3.9 31.9 - - - +
133A ALA 3.2 6.1 + - - +
134A PRO* 1.3 79.5 - - - +
136A TYR* 1.3 68.6 + - - +
137A ALA* 3.4 8.7 - - + +
138A LYS* 3.3 30.2 - - + +
139A MET* 3.6 4.7 + - - +
246A LEU* 5.8 0.5 - - - +
366A ASP* 4.9 5.8 - - + +
367A ARG 4.5 1.4 + - - -
371A PHE* 4.7 0.3 - - - -
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Residues in contact with TYR 136 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92A GLU* 4.2 9.1 + - - -
115A LEU* 3.2 61.0 + - + +
116A ALA* 3.8 5.8 - - - -
117A ALA 5.5 1.8 - - - +
134A PRO 5.5 0.4 - - - -
135A ALA* 1.3 71.1 - - - +
137A ALA* 1.3 58.2 + - - +
138A LYS 2.9 1.8 - - - -
139A MET* 2.6 38.6 + - + +
140A GLY* 3.0 8.3 + - - -
167A ASN* 4.3 12.2 + - - +
170A PHE* 3.7 27.1 - - + +
171A THR* 3.5 53.2 + - + +
174A GLY* 4.1 9.8 - - - -
246A LEU* 4.1 17.7 - - + -
247A PHE* 4.7 8.2 - + - -
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Residues in contact with ALA 137 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115A LEU 4.9 0.8 + - - -
117A ALA* 5.2 7.0 - - + +
120A GLN* 3.5 30.3 - - - +
135A ALA* 4.3 6.5 - - + +
136A TYR* 1.3 78.2 - - - +
138A LYS* 1.3 66.3 + - + +
140A GLY* 3.1 2.6 + - - -
141A GLU* 2.9 25.1 + - - +
174A GLY* 4.0 18.4 - - - -
177A GLU* 5.6 3.6 - - + -
178A VAL* 3.6 15.4 - - + +
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Residues in contact with LYS 138 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134A PRO* 4.3 4.0 - - + -
135A ALA* 3.3 30.5 - - + +
136A TYR 2.7 4.2 + - - -
137A ALA* 1.3 76.6 - - - +
139A MET* 1.3 54.2 + - - +
141A GLU* 2.7 54.4 + - - +
142A MET* 3.1 4.9 + - - +
362A ASP* 3.0 30.9 + - - +
366A ASP* 4.1 13.2 - - - +
367A ARG 3.8 20.9 - - - +
368A TYR* 4.8 12.9 - - + +
369A GLY 4.7 9.6 - - - +
371A PHE* 3.8 16.0 - - + -
390A TYR* 5.2 1.0 - - - -
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Residues in contact with MET 139 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135A ALA 3.6 1.8 + - - +
136A TYR* 2.6 25.3 + - + +
138A LYS* 1.3 74.3 - - - +
140A GLY* 1.3 55.5 + - - +
141A GLU 3.2 0.2 - - - -
142A MET* 3.4 4.5 + - - +
143A MET* 3.1 29.0 + - - +
171A THR* 3.5 43.1 - - + +
175A VAL* 4.2 14.4 - - + -
244A ILE* 3.5 29.8 - - + -
246A LEU* 4.1 12.8 - - + -
277A VAL* 4.8 8.1 - - + -
371A PHE* 3.2 38.5 - - + -
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Residues in contact with GLY 140 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136A TYR 3.0 8.6 + - - -
137A ALA 3.1 4.7 + - - -
138A LYS 3.0 1.2 - - - -
139A MET* 1.3 77.0 - - - +
141A GLU* 1.3 60.9 + - - +
142A MET 3.0 2.0 - - - -
143A MET* 3.8 6.4 - - - +
144A LEU* 2.9 29.1 + - - +
174A GLY 4.3 3.6 - - - -
175A VAL* 4.1 25.4 - - - -
178A VAL* 3.3 9.6 - - - +
179A PHE* 4.1 1.7 - - - -
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Residues in contact with GLU 141 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137A ALA* 2.9 18.8 + - - +
138A LYS* 2.7 38.6 + - - +
140A GLY* 1.3 77.9 - - - +
142A MET* 1.3 55.8 + - - +
144A LEU* 3.6 6.5 - - + +
145A ALA* 3.1 24.9 + - - +
178A VAL* 4.2 18.4 - - + +
368A TYR* 5.9 2.4 - - - -
390A TYR* 3.8 13.0 + - + +
392A GLY* 6.1 0.9 - - - -
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Residues in contact with MET 142 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138A LYS 3.1 3.8 + - - +
139A MET 3.4 11.2 - - - +
141A GLU* 1.3 74.7 - - - +
143A MET* 1.3 62.0 + - - +
144A LEU 3.1 1.1 - - - -
145A ALA* 2.8 5.2 + - - +
146A LEU* 2.6 56.7 + - + +
277A VAL* 3.5 27.1 - - + -
371A PHE* 3.9 22.2 - - + +
372A SER 5.3 0.2 - - - -
373A VAL* 3.5 32.3 - - + -
390A TYR* 3.3 43.5 - - + -
397A PHE* 4.6 9.6 - - + -
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Residues in contact with MET 143 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139A MET* 3.1 29.0 + - - +
140A GLY* 3.5 4.2 + - - +
142A MET* 1.3 85.9 - - - +
144A LEU* 1.3 53.9 + - - +
146A LEU* 4.0 12.3 - - + -
147A PHE* 2.7 49.7 + - + +
175A VAL* 4.6 7.0 - - + -
179A PHE* 3.9 18.4 - - + -
214A ILE* 3.4 44.2 - - + -
242A PHE* 4.4 16.6 - - + -
244A ILE* 5.4 0.4 - - - -
277A VAL* 3.9 24.7 - - + -
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Residues in contact with LEU 144 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140A GLY 2.9 18.8 + - - +
141A GLU* 3.6 7.4 - - + +
143A MET* 1.3 77.5 - - - +
145A ALA* 1.3 58.5 + - + +
147A PHE* 3.3 1.9 + - - +
148A ARG* 2.9 79.6 + - + +
178A VAL* 3.6 15.0 - - + -
179A PHE* 3.5 9.3 - - + -
182A GLU* 4.0 25.1 - - + -
184A LEU* 3.5 32.1 - - + -
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Residues in contact with ALA 145 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141A GLU 3.1 14.1 + - - +
142A MET 2.8 8.1 + - - +
144A LEU* 1.3 79.1 - - + +
146A LEU* 1.3 67.7 + - - +
148A ARG* 2.8 23.1 + - - +
149A HIS* 3.1 11.0 + - - +
390A TYR* 3.7 30.3 - - + +
395A GLY 5.9 0.2 - - - +
397A PHE* 5.0 6.1 - - + -
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Residues in contact with LEU 146 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142A MET* 2.6 44.1 + - + +
143A MET* 3.5 17.5 - - + +
145A ALA* 1.3 71.0 - - - +
147A PHE* 1.3 62.8 + - + +
149A HIS* 3.0 25.4 + - + +
150A HIS* 3.4 31.6 + - + +
152A TRP* 5.5 1.8 - - + -
242A PHE* 4.0 29.4 - - + -
275A GLN* 4.8 2.9 - - - +
277A VAL* 5.1 0.2 - - + -
373A VAL* 4.3 9.9 - - + -
397A PHE* 4.1 31.2 - - + -
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Residues in contact with PHE 147 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143A MET* 2.7 38.5 + - + +
144A LEU* 3.4 7.4 - - - +
146A LEU* 1.3 72.0 - - + +
148A ARG* 1.3 60.0 + - + +
149A HIS 2.9 6.8 + - - -
150A HIS* 3.4 1.2 + - - -
151A HIS* 3.0 18.0 + - - -
152A TRP* 3.2 58.4 + + + +
153A SER* 4.6 0.4 - - - -
154A ARG 3.5 23.6 - - - -
155A ALA* 3.6 20.2 - - + -
179A PHE* 3.9 14.1 - + - -
184A LEU* 4.2 15.0 - - + -
212A VAL* 3.6 23.1 - - + -
214A ILE* 3.7 21.5 - - + -
242A PHE* 5.2 1.3 - + - -
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Residues in contact with ARG 148 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144A LEU* 2.9 48.6 + - + +
145A ALA* 2.8 17.7 + - - +
147A PHE* 1.3 72.7 - - + +
149A HIS* 1.3 59.7 + - - +
151A HIS* 3.5 21.7 - - - +
152A TRP 5.0 2.9 - - - +
182A GLU* 3.5 22.4 + - - -
184A LEU* 5.7 4.7 - - + -
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Residues in contact with HIS 149 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145A ALA 3.1 8.0 + - - +
146A LEU* 3.0 20.0 - - + +
147A PHE 2.9 1.2 - - - -
148A ARG* 1.3 75.6 - - - +
150A HIS* 1.3 68.5 + + - +
151A HIS* 2.9 26.1 + - - -
397A PHE* 4.0 31.5 - + + -
399A MET* 4.6 20.6 - - + +
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Residues in contact with HIS 150 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146A LEU* 3.4 32.7 + - + +
147A PHE 3.4 1.1 + - - +
149A HIS* 1.3 87.9 + - - +
151A HIS* 1.3 71.6 + - - +
152A TRP* 3.1 62.1 + + + +
242A PHE* 5.6 0.2 - + - -
275A GLN* 5.3 11.6 + - - -
387A ILE* 6.5 0.4 - - + -
397A PHE* 5.9 0.7 - + - -
399A MET* 6.3 4.9 - - + -
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Residues in contact with HIS 151 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147A PHE 3.0 5.9 + - - -
148A ARG* 3.5 19.4 + - - +
149A HIS 2.9 17.9 + - - -
150A HIS* 1.3 81.2 + - - +
152A TRP* 1.3 67.0 + - - +
153A SER* 3.8 3.5 + - - -
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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