Contacts of the helix formed by residues 135 - 152 (chain A) in PDB entry 1SEK
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 PHE 135 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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107A TYR* 3.7 21.5 - - + -
108A VAL 3.6 5.8 - - - -
109A ALA* 3.4 34.3 - - + +
110A LYS 5.0 1.2 - - - +
133A VAL* 3.3 25.7 + - + -
134A ASP* 1.3 69.9 + - - +
136A VAL* 1.3 66.2 + - + +
137A LYS 3.0 2.7 - - - -
138A SER* 2.9 14.8 + - - -
141A ALA* 4.1 10.1 - - + -
145A ILE* 4.3 12.1 - - + -
166A LEU* 3.9 30.5 - - + -
167A ASP 3.3 25.7 - - - +
168A GLU* 3.6 5.9 - - - +
170A THR* 3.2 37.0 - - + +
171A ARG 3.8 8.1 - - - -
173A VAL* 4.3 5.8 - - + -
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Residues in contact with VAL 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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134A ASP* 3.0 23.5 + - - +
135A PHE* 1.3 79.5 - - + +
137A LYS* 1.3 60.2 + - + +
138A SER* 3.3 4.7 + - - -
168A GLU* 3.8 47.4 + - + +
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Residues in contact with LYS 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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134A ASP* 3.3 32.5 + - + +
135A PHE 3.0 1.7 - - - -
136A VAL* 1.3 79.6 - - + +
138A SER* 1.3 65.1 + - - +
139A VAL 3.4 2.2 - - - -
140A GLU* 2.9 45.1 + - + +
141A ALA* 2.9 11.1 + - - +
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Residues in contact with SER 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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135A PHE* 2.9 14.1 + - - +
136A VAL 4.0 5.7 + - - -
137A LYS* 1.3 72.4 - - - +
139A VAL* 1.3 63.6 + - - +
141A ALA* 2.9 8.4 + - - +
142A ALA* 2.8 30.0 + - - +
163A PRO 4.2 9.2 - - - -
166A LEU* 3.8 29.8 - - - +
167A ASP* 4.7 2.5 - - - -
168A GLU* 4.5 12.3 + - - +
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Residues in contact with VAL 139 (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 LYS 3.4 0.8 - - - -
138A SER* 1.3 80.3 + - - +
140A GLU* 1.3 57.2 + - - +
142A ALA* 3.5 1.9 + - - +
143A GLY* 3.0 24.1 + - - -
163A PRO* 4.0 32.0 - - + +
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Residues in contact with GLU 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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134A ASP 5.8 0.7 - - - +
137A LYS* 2.9 43.1 + - + +
139A VAL* 1.3 74.5 - - - +
141A ALA* 1.3 62.4 + - - +
143A GLY* 3.3 2.6 + - - -
144A ALA* 2.9 28.7 + - + +
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Residues in contact with ALA 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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133A VAL* 4.3 11.4 - - + -
134A ASP 3.6 22.7 - - - +
135A PHE* 4.1 17.7 - - + -
137A LYS 2.9 6.3 + - - +
138A SER* 3.3 9.2 - - - +
140A GLU* 1.3 75.1 - - - +
142A ALA* 1.3 58.8 + - - +
144A ALA* 3.0 9.2 + - - +
145A ILE* 2.8 35.7 + - - +
166A LEU* 4.1 11.4 - - + -
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Residues in contact with ALA 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 SER 2.8 14.6 + - - +
139A VAL 3.8 4.3 - - - +
141A ALA* 1.3 76.2 - - - +
143A GLY* 1.3 57.2 + - - +
145A ILE* 3.2 1.8 + - - +
146A ASN* 2.8 38.0 + - - +
161A VAL* 4.0 16.4 - - + +
162A ASP 4.4 0.2 - - - -
163A PRO* 3.7 36.3 - - + -
166A LEU* 3.6 14.0 - - + +
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Residues in contact with GLY 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 VAL 3.0 14.9 + - - -
140A GLU* 3.3 4.7 + - - -
142A ALA* 1.3 77.5 - - - +
144A ALA* 1.3 56.6 + - - +
146A ASN* 3.8 6.9 - - - +
147A LYS* 3.0 31.9 + - - +
163A PRO* 5.7 0.2 - - - +
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Residues in contact with ALA 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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107A TYR* 4.3 4.2 + - + -
131A GLN* 6.0 0.4 - - - +
133A VAL* 4.3 16.6 - - + -
140A GLU* 2.9 15.9 + - + +
141A ALA* 3.0 12.7 + - - +
143A GLY* 1.3 74.7 - - - +
145A ILE* 1.3 64.8 + - + +
147A LYS* 3.3 6.7 + - - +
148A TRP* 3.2 21.8 + - - +
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Residues in contact with ILE 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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107A TYR* 3.8 47.6 - - + -
133A VAL* 5.2 2.2 - - + -
135A PHE* 4.3 21.1 - - + -
141A ALA* 2.8 20.4 + - - +
144A ALA* 1.3 77.7 - - + +
146A ASN* 1.3 59.6 + - - +
148A TRP* 3.4 4.0 + - - +
149A VAL* 3.2 26.3 + - + +
160A LEU* 4.8 0.2 - - + -
161A VAL* 3.6 27.1 - - + -
166A LEU* 4.6 8.7 - - + -
173A VAL* 4.5 12.3 - - + -
175A VAL* 3.7 24.2 - - + -
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Residues in contact with ASN 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 ALA* 2.8 25.8 + - - +
143A GLY* 4.0 6.6 - - - +
145A ILE* 1.3 71.1 - - - +
147A LYS* 1.3 64.6 + - - +
149A VAL* 3.7 5.7 + - - +
150A GLU* 3.2 30.9 + - + +
157A ILE 5.1 0.2 - - - +
158A LYS* 5.2 0.3 - - - -
159A ASN* 3.6 25.0 + - - +
160A LEU* 2.9 15.0 + - - +
161A VAL* 2.8 51.4 + - - +
163A PRO* 5.3 1.8 - - - +
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Residues in contact with LYS 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 GLY 3.0 19.3 + - - +
144A ALA* 3.7 6.5 - - - +
145A ILE 3.2 0.4 - - - -
146A ASN* 1.3 76.3 - - - +
148A TRP* 1.3 64.2 + - - +
150A GLU* 3.3 22.4 + - - +
151A ASP* 3.0 45.4 + - - +
155A ASN* 5.9 2.3 - - - +
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Residues in contact with TRP 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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103A ALA* 3.6 25.4 - - + -
104A SER 3.7 15.3 - - - -
105A LYS* 3.4 36.8 - - + +
107A TYR* 3.3 26.5 - + - +
129A GLU* 3.0 22.3 + - + -
144A ALA 3.2 7.6 + - - +
145A ILE 3.8 3.4 - - - +
146A ASN 3.4 0.2 - - - -
147A LYS* 1.3 80.5 - - - +
149A VAL* 1.3 83.5 + - + +
151A ASP* 3.2 11.4 + - + +
152A GLN* 2.9 53.0 + - + +
175A VAL* 3.7 24.2 - - + -
177A ALA* 5.8 1.6 - - + -
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Residues in contact with VAL 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 ILE* 3.2 22.8 + - + +
146A ASN* 3.9 5.2 - - - +
147A LYS 3.3 0.2 - - - -
148A TRP* 1.3 97.7 - - + +
150A GLU* 1.3 66.7 + - - +
152A GLN* 3.0 5.2 + - + +
153A THR* 3.0 27.3 + - + +
157A ILE* 3.9 25.4 - - + +
158A LYS* 5.7 0.9 - - - -
160A LEU* 4.3 27.4 - - + -
175A VAL* 4.9 0.9 - - + -
177A ALA* 3.8 25.8 - - + -
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Residues in contact with GLU 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 ASN* 3.2 17.3 + - - +
147A LYS* 3.4 37.0 + - - +
149A VAL* 1.3 78.5 - - - +
151A ASP* 1.3 64.1 + - - +
153A THR* 3.3 1.4 + - - -
154A ASN* 3.2 3.8 + - - -
155A ASN* 2.6 57.3 + - - +
157A ILE 3.4 22.2 - - - +
158A LYS* 3.5 26.6 + - + +
159A ASN 5.1 0.4 + - - -
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Residues in contact with ASP 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 LYS* 3.0 35.5 + - - +
148A TRP* 3.4 13.7 - - + +
149A VAL 3.1 0.2 - - - -
150A GLU* 1.3 81.0 - - - +
152A GLN* 1.3 67.1 + - - +
153A THR 3.5 0.3 + - - -
154A ASN* 3.9 8.4 + - - +
155A ASN* 5.2 4.7 + - - -
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Residues in contact with GLN 152 (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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101A LYS* 3.5 21.8 + - - +
103A ALA* 3.7 31.7 - - + +
148A TRP* 2.9 42.1 + - + +
149A VAL* 3.0 7.8 + - - +
151A ASP* 1.3 81.8 + - - +
153A THR* 1.3 61.5 + - + +
154A ASN* 3.7 2.2 + - - -
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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