Contacts of the helix formed by residues 128 - 144 (chain A) in PDB entry 2R8K
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 LEU 128 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35A PHE* 3.6 21.8 - - + -
55A GLN* 4.8 5.8 - - - +
60A ILE* 5.6 0.2 - - + -
92A THR* 5.2 1.3 - - + -
126A VAL* 4.0 17.5 - - + +
127A SER* 1.3 84.8 + - - +
129A GLU* 1.3 66.0 + - - +
130A PRO 3.3 2.7 - - - -
131A TYR* 3.3 28.4 + - + +
132A ARG* 3.0 42.9 + - + +
154A ILE* 5.9 2.7 - - + -
422A GLU* 6.0 1.2 - - - -
6U C 6.0 5.4 - - - +
7U T 6.0 7.2 - - - -
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Residues in contact with GLU 129 (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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102A TRP* 3.0 39.8 + - - +
127A SER* 3.5 4.4 + - - +
128A LEU* 1.3 76.6 - - - +
130A PRO* 1.3 59.3 - - + +
132A ARG* 2.6 27.0 + - + +
133A ARG* 2.5 62.5 + - + +
425A SER* 2.6 34.9 + - - +
428A GLN* 5.1 3.8 - - - +
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Residues in contact with PRO 130 (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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38A VAL* 5.2 2.9 - - + -
39A GLU* 5.0 0.2 - - - +
93A ALA* 4.4 4.0 - - + -
102A TRP* 3.5 35.0 - - + -
104A TYR* 3.6 28.0 - - + +
127A SER* 4.2 9.0 - - - +
128A LEU* 3.4 6.3 - - - +
129A GLU* 1.3 94.9 - - + +
131A TYR* 1.3 69.3 + - + +
133A ARG* 3.4 9.9 + - + +
134A GLU* 3.1 29.8 + - - +
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Residues in contact with TYR 131 (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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34A PHE* 3.4 13.1 - - + -
35A PHE* 3.2 69.5 - + + -
38A VAL* 3.2 24.9 - - + -
39A GLU* 2.9 28.7 + - - -
53A CYS* 3.6 6.2 - - - -
92A THR* 3.2 30.8 - - + +
93A ALA 5.5 0.4 - - - -
104A TYR* 3.9 4.4 + - - -
127A SER 3.9 9.4 - - - -
128A LEU* 3.3 30.0 + - + +
129A GLU 3.1 0.4 - - - -
130A PRO* 1.3 76.2 - - + +
132A ARG* 1.3 60.5 + - - +
134A GLU* 4.7 1.3 - - - -
135A SER* 3.0 27.7 + - - -
154A ILE* 4.1 4.9 - - + -
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Residues in contact with ARG 132 (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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127A SER* 5.4 0.2 + - - -
128A LEU* 3.0 26.3 + - + +
129A GLU* 2.6 54.5 + - + +
131A TYR* 1.3 70.3 - - - +
133A ARG* 1.3 65.8 + - + +
135A SER* 3.0 17.6 + - - -
136A ARG* 3.1 18.5 + - - +
151A ARG* 5.4 5.8 - - - +
154A ILE* 4.1 16.4 - - + -
422A GLU* 4.4 14.6 + - - +
425A SER* 4.0 13.9 + - - -
426A ARG* 3.7 40.0 - - - +
429A ASP* 4.6 26.0 - - - +
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Residues in contact with ARG 133 (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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102A TRP* 5.7 2.5 - - + -
129A GLU* 2.5 61.1 + - + +
130A PRO* 3.5 10.3 - - + +
132A ARG* 1.3 73.5 - - - +
134A GLU* 1.3 66.2 + - - +
136A ARG* 3.8 5.4 + - - +
137A LYS* 3.5 38.8 + - - +
429A ASP* 5.6 1.6 - - - -
195B ILE 5.1 0.6 + - - -
196B GLY* 3.5 25.9 + - - -
197B GLY* 5.1 3.4 - - - -
198B ASN* 3.6 18.0 + - - +
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Residues in contact with GLU 134 (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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34A PHE* 4.2 8.7 - - + -
38A VAL* 4.1 11.7 - - + -
130A PRO 3.1 17.6 + - - +
131A TYR 4.0 3.1 - - - +
133A ARG* 1.3 80.7 + - - +
135A SER* 1.3 67.9 + - - +
137A LYS* 2.8 53.3 + - - +
138A ALA* 3.1 12.6 + - - +
256A LEU* 4.5 5.0 - - - +
258A TYR* 2.7 42.3 + - + +
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Residues in contact with SER 135 (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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31A MET* 4.8 1.9 - - - +
34A PHE* 3.8 10.2 - - - -
131A TYR 3.0 18.6 + - - -
132A ARG 3.0 6.3 + - - -
134A GLU* 1.3 76.2 - - - +
136A ARG* 1.3 62.6 + - - +
138A ALA* 3.4 8.1 + - - +
139A LEU* 3.0 19.1 + - - +
151A ARG* 3.0 23.5 + - - -
154A ILE* 2.5 38.7 + - - -
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Residues in contact with ARG 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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132A ARG* 3.1 11.5 + - - +
133A ARG* 3.9 5.4 - - - +
135A SER* 1.3 76.3 - - - +
137A LYS* 1.3 67.8 + - - +
139A LEU* 2.6 27.5 + - + +
140A LYS* 2.7 40.4 + - + +
151A ARG* 3.6 22.8 - - - +
429A ASP* 2.7 46.3 + - - +
432A GLN* 4.4 19.7 + - - -
433A GLU* 2.8 53.8 + - - +
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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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133A ARG* 3.5 32.0 + - - +
134A GLU* 2.8 46.4 + - - +
136A ARG* 1.3 76.2 - - + +
138A ALA* 1.3 66.5 + - - +
140A LYS* 2.7 26.2 + - - +
141A ILE* 2.9 14.5 + - + +
256A LEU* 3.6 20.1 - - + +
195B ILE* 3.7 45.4 - - + +
196B GLY* 5.0 2.5 - - - -
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Residues in contact with ALA 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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31A MET* 3.5 31.0 - - + -
134A GLU 3.1 6.2 + - - +
135A SER 3.4 9.4 - - - +
137A LYS* 1.3 78.2 - - - +
139A LEU* 1.3 62.0 + - - +
141A ILE* 3.2 6.4 + - - +
142A PHE* 2.8 39.0 + - + -
252A ILE* 4.3 10.1 - - + -
256A LEU* 3.4 17.6 - - + +
258A TYR* 5.2 0.2 - - + -
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Residues in contact with LEU 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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135A SER 3.0 12.6 + - - +
136A ARG* 2.6 33.7 + - + +
138A ALA* 1.3 69.1 - - - +
140A LYS* 1.3 58.7 + - + +
142A PHE* 2.8 21.6 + - + +
143A LYS* 2.9 40.6 + - + +
149A VAL* 4.0 20.4 - - + -
151A ARG* 3.9 36.3 - - + +
157A VAL* 3.8 27.8 - - + -
433A GLU* 4.5 4.3 - - + +
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Residues in contact with LYS 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 ARG* 2.7 43.1 + - + +
137A LYS* 2.7 12.7 + - - +
139A LEU* 1.3 72.7 - - - +
141A ILE* 1.3 60.7 + - + +
142A PHE 3.2 1.0 + - - -
143A LYS* 3.4 9.2 + - - +
144A SER* 3.3 21.7 + - - -
432A GLN* 3.4 15.3 + - - -
171B PHE* 3.7 7.6 - - + -
194B PHE* 2.7 58.5 + - + +
195B ILE* 4.0 13.6 + - + -
197B GLY* 3.8 9.5 - - - -
199B TYR* 3.4 17.5 + - - -
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Residues in contact with ILE 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 LYS* 2.9 13.2 + - + +
138A ALA* 3.4 9.0 - - - +
140A LYS* 1.3 76.0 - - + +
142A PHE* 1.3 60.5 + - - +
144A SER* 2.9 19.0 + - - +
145A ALA* 4.0 8.1 + - - +
248A ILE* 5.0 3.4 - - + +
251A SER* 4.0 23.3 - - - -
252A ILE* 3.6 22.4 - - + -
255A ILE* 3.8 26.0 - - + -
256A LEU* 3.5 40.2 - - + -
171B PHE* 3.9 19.7 - - + -
195B ILE* 5.4 6.1 - - + -
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Residues in contact with PHE 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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29A ILE* 3.7 31.2 - - + -
31A MET* 5.3 6.3 - - + -
138A ALA* 2.8 39.0 + - + -
139A LEU* 2.8 13.8 + - - +
141A ILE* 1.3 73.6 - - - +
143A LYS* 1.3 52.7 - - - +
144A SER 2.7 5.1 + - - -
145A ALA* 2.7 29.3 + - - +
146A CYS* 3.0 12.0 + - - +
149A VAL* 4.3 18.6 - - + -
157A VAL* 3.8 31.0 - - + -
159A LEU* 4.2 13.9 - - + -
248A ILE* 3.4 31.2 - - + -
249A ARG* 5.6 0.7 - - + -
252A ILE* 3.6 21.8 - - + -
260A THR* 5.9 1.6 - - + -
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Residues in contact with LYS 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 LEU* 2.9 47.6 + - + +
140A LYS* 4.1 7.9 - - + +
142A PHE* 1.3 71.3 - - - +
144A SER* 1.3 57.8 + - - +
145A ALA 3.3 0.4 - - - -
146A CYS 3.4 21.0 + - - +
147A ASP* 5.2 0.9 - - - -
149A VAL* 4.2 23.3 - - + +
433A GLU* 4.5 20.2 + - - +
167B ASN* 4.4 6.2 + - - +
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Residues in contact with SER 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 LYS 3.3 4.9 + - - -
141A ILE* 2.9 19.6 + - - +
142A PHE 2.7 3.6 + - - -
143A LYS* 1.3 76.0 - - - +
145A ALA* 1.3 59.9 + - - +
146A CYS 3.6 0.2 - - - -
167B ASN* 3.8 30.4 + - - +
171B PHE* 3.4 52.6 - - - +
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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