Contacts of the helix formed by residues 144 - 157 (chain A) in PDB entry 4X4U
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 LYS 144 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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140A ARG 4.3 16.2 - - - +
141A ILE* 2.9 15.3 + - + +
142A LYS 4.6 3.1 - - - +
143A GLY* 1.3 85.7 - - - +
145A GLU* 1.3 64.9 + - - +
146A ASN 3.2 3.1 - - - -
147A GLU* 2.8 24.1 + - + +
148A VAL* 3.1 13.5 + - - +
179A ILE* 4.0 23.3 - - + +
180A VAL* 4.9 7.4 - - + +
183A GLY* 2.9 36.7 + - - +
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Residues in contact with GLU 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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50A ARG 3.4 16.5 - - - +
51A ASN* 3.2 35.0 - - + +
52A THR* 3.9 12.4 - - + +
141A ILE* 3.7 7.1 + - + +
142A LYS* 3.4 15.8 + - - +
143A GLY* 3.0 30.3 + - - -
144A LYS* 1.3 77.2 + - - +
146A ASN* 1.3 60.3 + - - +
148A VAL* 3.2 6.7 + - - +
149A ARG* 3.0 36.9 + - - +
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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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11A LEU* 3.9 21.7 - - + +
15A ILE* 3.2 32.8 - - - +
144A LYS 3.2 1.0 - - - -
145A GLU* 1.3 76.0 - - - +
147A GLU* 1.3 65.3 + - + +
149A ARG* 3.3 23.1 + - - +
150A LEU* 2.9 33.3 + - - +
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Residues in contact with GLU 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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7A LEU* 6.0 0.7 - - - +
143A GLY 5.5 0.7 - - - +
144A LYS* 2.8 20.2 + - + +
146A ASN* 1.3 79.7 - - + +
148A VAL* 1.3 63.0 + - - +
150A LEU* 3.4 14.7 + - - +
151A LEU 3.1 17.2 + - - -
179A ILE* 3.5 28.2 - - + +
183A GLY 4.4 3.4 - - - +
184A SER* 3.4 18.8 - - - -
185A PHE* 2.7 38.4 + - - +
186A LEU* 4.2 1.4 + - - +
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Residues in contact with VAL 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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52A THR* 3.9 14.1 - - + -
141A ILE* 3.5 34.3 - - + -
144A LYS 3.1 14.0 + - - +
145A GLU 3.4 7.2 - - - +
147A GLU* 1.3 77.9 - - - +
149A ARG* 1.3 61.2 + - - +
151A LEU* 3.3 3.2 + - - +
152A LYS* 3.0 43.4 + - + +
175A CYS* 4.7 1.1 - - + +
176A GLU* 3.6 30.3 - - + +
179A ILE* 3.9 17.9 - - + -
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Residues in contact with ARG 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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14A VAL* 3.1 38.8 - - + +
15A ILE* 4.1 14.5 - - + +
16A PRO* 3.6 17.9 - - - +
51A ASN* 2.6 59.3 + - - +
52A THR 3.6 15.6 - - - +
53A TRP* 2.7 33.2 + - - +
54A LEU* 3.5 4.6 - - + +
145A GLU* 3.0 24.0 + - - +
146A ASN* 3.3 26.1 + - - +
148A VAL* 1.3 75.0 - - - +
150A LEU* 1.3 57.6 + - - +
152A LYS* 3.4 4.6 + - - -
153A GLY* 3.0 24.1 + - - -
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Residues in contact with LEU 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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7A LEU* 3.9 21.3 - - + +
10A ALA* 3.7 36.3 - - + +
11A LEU* 3.7 27.6 - - + -
14A VAL* 4.1 4.7 - - + -
146A ASN 2.9 19.7 + - - +
147A GLU* 3.6 25.1 - - - +
148A VAL 3.2 0.2 - - - -
149A ARG* 1.3 74.8 - - - +
151A LEU* 1.3 64.6 + - - +
153A GLY 3.5 0.3 + - - -
154A PHE* 3.0 24.9 + - - +
185A PHE* 3.9 20.6 - - + -
254A PHE* 3.5 14.4 - - + -
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Residues in contact with LEU 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 GLU 3.1 14.0 + - - +
148A VAL 3.7 7.2 - - - +
150A LEU* 1.3 75.1 - - - +
152A LYS* 1.3 63.8 + - - +
154A PHE* 3.2 4.6 + - + +
155A LEU* 3.0 42.1 + - + +
175A CYS* 3.6 41.1 - - + +
178A LEU* 4.2 17.3 - - + -
179A ILE* 4.0 13.2 - - + -
185A PHE* 3.5 26.2 - - + -
188A THR* 4.4 10.5 - - + -
189A VAL* 5.5 0.2 - - + -
238A PHE* 4.3 22.2 - - + -
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Residues in contact with LYS 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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47A SER* 3.2 31.3 + - - -
52A THR* 3.3 20.8 + - - +
53A TRP* 4.5 2.0 - - - +
54A LEU* 4.1 20.1 - - + +
148A VAL* 3.0 33.3 + - - +
149A ARG* 3.7 4.7 - - - +
151A LEU* 1.3 76.7 - - - +
153A GLY* 1.3 51.7 - - - +
155A LEU* 3.2 5.1 + - - +
156A LYS* 2.7 38.3 + - - +
161A TYR* 3.5 44.5 + - + +
172A GLY* 3.9 21.1 - - - -
175A CYS* 4.2 8.5 - - + -
176A GLU* 4.4 4.0 + - - -
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Residues in contact with GLY 153 (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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14A VAL* 4.1 10.5 - - - -
54A LEU* 3.8 19.6 - - - +
149A ARG 3.0 16.0 + - - -
150A LEU 4.0 0.9 - - - -
152A LYS* 1.3 77.1 - - - +
154A PHE* 1.3 56.7 + - - +
156A LYS* 3.6 2.5 - - - +
157A ALA* 2.8 32.4 + - - +
254A PHE* 4.3 8.9 - - - +
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Residues in contact with PHE 154 (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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150A LEU 3.0 18.5 + - - +
151A LEU* 3.3 5.8 - - + +
152A LYS 3.2 0.2 - - - -
153A GLY* 1.3 78.5 - - - +
155A LEU* 1.3 60.0 + - - +
157A ALA 3.6 0.5 + - - -
158A ASN* 2.6 33.5 + - - +
185A PHE* 3.8 19.5 - + + -
189A VAL* 4.9 2.5 - - + -
238A PHE* 3.9 30.1 - + - -
241A LEU* 4.1 33.7 - - + -
242A CYS* 4.7 6.5 - - - -
245A PHE* 4.0 24.7 - + + -
253A PHE* 3.6 38.8 - + + -
254A PHE* 3.7 26.8 - + + -
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Residues in contact with LEU 155 (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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151A LEU* 3.0 27.4 + - + +
152A LYS* 3.6 4.0 - - - +
154A PHE* 1.3 75.6 - - + +
156A LYS* 1.3 65.7 + - - +
158A ASN 3.1 6.1 + - - -
160A ILE* 3.0 50.5 + - + +
161A TYR* 3.8 13.9 - - + -
170A PHE* 3.5 40.6 - - + -
175A CYS* 3.4 33.4 - - - -
238A PHE* 3.6 23.6 - - + -
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Residues in contact with LYS 156 (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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54A LEU* 4.0 14.4 - - + -
57A SER* 4.5 16.9 + - - -
152A LYS 2.7 22.3 + - - +
153A GLY* 3.6 9.6 - - - +
155A LEU* 1.3 74.2 - - - +
157A ALA* 1.3 58.8 + - - +
158A ASN 3.1 5.0 + - - -
159A GLY* 3.2 12.0 + - - -
161A TYR* 3.6 35.4 + - + +
164A GLU* 5.9 0.8 + - - -
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Residues in contact with ALA 157 (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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153A GLY 2.8 17.3 + - - +
154A PHE 3.6 0.2 + - - -
155A LEU 3.3 0.2 - - - -
156A LYS* 1.3 76.2 - - - +
158A ASN* 1.3 62.8 + - - +
159A GLY 3.6 0.4 - - - -
253A PHE 3.6 11.4 - - - +
254A PHE 3.4 31.9 - - - +
255A LYS 3.7 18.3 - - - +
256A PRO* 4.0 16.9 - - + +
257A LYS* 4.0 10.7 - - - +
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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
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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