Contacts of the helix formed by residues 152 - 170 (chain B) in PDB entry 4XCS
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 SER 152 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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59B PHE* 4.7 0.7 - - - -
150B GLY 3.6 2.0 + - - -
151B ARG* 1.3 71.7 - - - +
153B VAL* 1.3 58.3 + - - +
154B ASP* 3.3 9.9 + - - +
155B GLU* 3.0 44.8 + - - +
156B THR* 2.7 30.8 + - - -
25C GLN* 3.5 22.4 + - - -
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Residues in contact with VAL 153 (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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58B ALA* 3.6 41.3 - - + +
59B PHE* 3.8 24.9 - - + -
62B ARG* 3.6 39.5 - - + +
66B PHE* 3.8 24.5 - - + -
151B ARG 3.6 2.5 + - - +
152B SER* 1.3 71.8 + - - +
154B ASP* 1.3 64.5 + - - +
156B THR* 3.0 2.4 + - - -
157B LEU* 2.9 24.9 + - + +
25C GLN* 5.5 1.6 - - - +
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Residues in contact with ASP 154 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62B ARG* 2.8 39.9 + - - +
152B SER* 3.3 6.9 + - - +
153B VAL* 1.3 78.3 - - - +
155B GLU* 1.3 63.5 + - - +
157B LEU* 3.4 5.7 + - - +
158B ARG* 3.1 46.2 + - - +
27C LYS* 4.9 18.9 - - - +
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Residues in contact with GLU 155 (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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155A GLU* 3.1 39.7 - - - +
158A ARG* 3.8 15.0 + - - +
152B SER* 3.0 30.5 + - - +
154B ASP* 1.3 78.2 - - - +
156B THR* 1.3 59.1 + - - +
158B ARG* 3.4 28.3 + - - +
159B LEU* 2.9 28.8 + - - +
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Residues in contact with THR 156 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40B VAL* 4.1 23.1 - - + -
59B PHE* 3.7 31.0 - - + -
66B PHE* 4.2 7.9 - - + -
130B LEU* 4.5 14.6 - - + +
132B ILE* 4.7 6.7 - - + -
151B ARG* 3.9 11.3 - - - +
152B SER 2.7 21.0 + - - -
153B VAL 3.0 5.3 + - - -
155B GLU* 1.3 78.1 - - - +
157B LEU* 1.3 62.9 + - - +
159B LEU* 3.2 8.3 + - + +
160B VAL* 3.0 22.2 + - - +
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Residues in contact with LEU 157 (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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62B ARG* 3.4 29.4 - - - +
65B GLU* 3.5 26.7 - - + +
66B PHE* 3.5 42.8 - - + -
69B LEU* 3.7 19.9 - - + +
153B VAL* 2.9 20.4 + - + +
154B ASP* 3.6 7.4 - - - +
156B THR* 1.3 76.5 - - - +
158B ARG* 1.3 63.7 + - - +
160B VAL* 3.2 5.1 + - - +
161B GLN* 2.9 31.8 + - - +
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Residues in contact with ARG 158 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155A GLU* 4.1 10.4 + - - -
158A ARG* 5.0 7.9 - - - +
154B ASP* 3.1 42.1 + - - +
155B GLU* 3.5 33.1 - - - +
157B LEU* 1.3 79.0 - - - +
159B LEU* 1.3 58.6 + - - +
161B GLN* 3.4 18.1 + - + +
162B ALA* 2.9 27.4 + - - +
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Residues in contact with LEU 159 (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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145A ASN* 5.0 0.4 - - - +
147A LEU* 3.6 22.2 - - + -
130B LEU* 4.6 7.6 - - + -
132B ILE* 3.8 24.5 - - + -
141B GLN* 3.3 35.9 - - - +
155B GLU 2.9 13.3 + - - +
156B THR* 3.3 11.9 - - - +
158B ARG* 1.3 76.8 - - - +
160B VAL* 1.3 64.2 + - - +
162B ALA* 3.1 5.2 + - + +
163B PHE* 2.9 48.5 + - + -
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Residues in contact with VAL 160 (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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38B TYR* 4.2 9.4 - - + -
40B VAL* 3.7 29.4 - - + -
66B PHE* 4.4 4.7 - - + -
69B LEU* 4.5 9.6 - - + -
71B CYS* 4.2 21.3 - - + -
132B ILE* 4.3 13.9 - - + -
156B THR 3.0 18.6 + - - +
157B LEU* 3.6 7.4 - - - +
159B LEU* 1.3 75.8 - - - +
161B GLN* 1.3 57.8 + - - +
163B PHE* 3.2 11.0 + - - +
164B GLN* 3.0 52.6 + - - +
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Residues in contact with GLN 161 (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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69B LEU* 4.0 31.4 - - + +
157B LEU* 2.9 16.4 + - - +
158B ARG* 3.4 31.5 + - + +
160B VAL* 1.3 76.7 - - - +
162B ALA* 1.3 55.8 - - - +
164B GLN* 3.3 7.3 + - - +
165B PHE* 2.9 32.7 + - - +
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Residues in contact with ALA 162 (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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147A LEU* 3.7 24.2 - - + -
149A VAL* 4.4 13.7 - - + -
158B ARG 2.9 14.1 + - - +
159B LEU* 3.1 9.6 + - + +
161B GLN* 1.3 76.5 - - - +
163B PHE* 1.3 61.2 + - - +
165B PHE* 3.6 5.2 + - - +
166B THR* 2.7 32.4 + - - +
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Residues in contact with PHE 163 (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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145A ASN* 4.0 1.6 - - + -
146A ASP* 3.9 1.8 - - - -
147A LEU* 3.7 31.2 - - + -
38B TYR* 3.3 21.8 - + + +
132B ILE* 4.0 19.3 - - + -
140B ARG* 3.6 64.8 - - + -
141B GLN* 3.7 14.4 - - + -
159B LEU* 2.9 51.1 + - + -
160B VAL 3.7 6.1 - - - +
162B ALA* 1.3 77.7 - - - +
164B GLN* 1.3 52.5 + - - +
166B THR* 3.0 4.7 + - - -
167B ASP* 2.7 39.5 + - - +
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Residues in contact with GLN 164 (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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38B TYR* 3.6 39.4 - - + +
69B LEU* 2.7 47.1 + - - +
70B ASN* 4.6 4.4 + - - +
160B VAL* 3.0 27.0 + - - +
161B GLN* 3.8 5.9 - - - +
163B PHE* 1.3 73.7 - - - +
165B PHE* 1.3 66.8 + - - +
167B ASP* 3.1 11.4 + - - +
168B LYS* 3.0 25.5 + - - +
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Residues in contact with PHE 165 (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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161B GLN 2.9 18.5 + - - +
162B ALA* 3.8 6.1 - - - +
164B GLN* 1.3 74.9 - - - +
166B THR* 1.3 59.6 + - + +
168B LYS* 3.0 5.3 + - - -
169B HIS* 2.8 67.7 + + + -
170B GLY 5.1 0.2 - - - -
172B VAL* 3.7 31.0 - - + -
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Residues in contact with THR 166 (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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147A LEU* 3.7 6.5 - - + +
148A PRO* 3.9 27.3 - - + +
149A VAL* 3.9 22.0 - - + -
140B ARG* 4.9 3.0 + - - -
162B ALA 2.7 22.4 + - - +
163B PHE* 3.0 14.2 + - - -
165B PHE* 1.3 72.0 - - + +
167B ASP* 1.3 66.3 + - - +
168B LYS 3.1 1.1 - - - -
170B GLY* 3.0 42.1 + - - +
172B VAL* 3.9 11.4 - - + +
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Residues in contact with ASP 167 (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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38B TYR* 2.6 31.9 + - - -
134B ASP* 4.4 3.9 - - - +
135B ASP* 4.3 6.2 - - - +
136B LYS* 6.0 5.2 - - - -
140B ARG* 2.2 33.3 + - - -
163B PHE 2.7 20.6 + - - +
164B GLN* 3.1 11.7 + - - +
166B THR* 1.3 75.5 + - - +
168B LYS* 1.3 61.6 + - + +
170B GLY 4.8 0.3 + - - -
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Residues in contact with LYS 168 (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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164B GLN 3.0 11.3 + - - +
165B PHE* 3.0 10.1 + - - +
167B ASP* 1.3 82.7 - - + +
169B HIS* 1.3 91.3 + - + +
170B GLY 3.8 0.2 - - - -
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Residues in contact with HIS 169 (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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165B PHE* 2.8 69.2 + + + +
168B LYS* 1.3 110.0 + - + +
170B GLY* 1.3 58.5 + - - +
171B GLU 4.9 1.2 - - - +
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Residues in contact with GLY 170 (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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148A PRO* 4.6 2.7 - - - -
165B PHE* 5.1 0.2 - - - -
166B THR* 3.0 35.8 + - - +
167B ASP 4.7 0.4 + - - -
168B LYS 3.8 0.8 - - - -
169B HIS* 1.3 82.0 - - - +
171B GLU* 1.3 67.9 + - - +
172B VAL* 3.3 4.9 + - - +
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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