Contacts of the helix formed by residues 144 - 156 (chain B) in PDB entry 1SG4
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 PRO 144 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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83B TRP* 3.8 15.3 - - + -
114B LEU* 6.0 0.2 - - + -
142B ILE 3.6 4.7 - - - +
143B ALA* 1.3 89.3 - - + +
145B PHE* 1.3 67.7 + - - +
146B TRP* 3.5 44.6 - - + +
147B LEU* 2.9 24.0 + - + -
148B LYS* 2.9 19.4 + - - +
231B ASP* 4.8 5.2 - - - +
701B CO8 4.0 23.8 - - + -
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Residues in contact with PHE 145 (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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143B ALA 3.7 1.0 + - - -
144B PRO* 1.3 73.9 - - - +
146B TRP* 1.3 88.3 + + + +
148B LYS* 3.3 6.7 + - - +
149B ASP* 2.8 33.7 + - - +
223B ARG* 3.5 66.0 - - + +
224B LEU* 3.9 5.6 - - + -
227B GLN* 3.5 39.3 - - + -
231B ASP* 3.5 25.4 - - + -
215C MET* 4.1 17.4 - - + -
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Residues in contact with TRP 146 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83B TRP* 3.5 25.4 - + - -
86B VAL* 3.9 24.7 - - + -
87B GLN* 4.2 11.2 - - + -
90B TRP* 3.4 63.5 - + + -
114B LEU* 3.6 16.2 - - + -
144B PRO* 3.5 21.3 - - + +
145B PHE* 1.3 103.9 - + + +
147B LEU* 1.3 76.5 + - + +
149B ASP* 3.7 8.1 - - - +
150B THR* 2.8 29.6 + - - -
220B THR 5.3 2.0 - - - +
224B LEU* 3.6 31.4 - - + +
231B ASP* 2.9 19.4 + - - -
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Residues in contact with LEU 147 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90B TRP* 4.7 5.2 - - + -
110B ALA 4.8 1.8 - - - +
111B GLY* 6.1 0.2 - - - -
114B LEU* 3.9 46.4 - - + -
117B LEU* 4.4 8.7 - - + -
134B LEU* 3.7 25.6 - - + -
136B GLU* 3.5 25.8 - - - +
143B ALA* 4.4 1.1 - - + -
144B PRO* 2.9 27.0 + - + +
146B TRP* 1.3 85.1 - - + +
148B LYS* 1.3 65.4 + - - +
150B THR* 3.2 11.5 + - + +
151B LEU* 2.9 23.7 + - - +
701B CO8 5.6 2.9 - - + -
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Residues in contact with LYS 148 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143B ALA* 4.4 4.1 - - + +
144B PRO 2.9 12.5 + - - +
145B PHE* 3.5 11.7 - - - +
147B LEU* 1.3 75.7 - - - +
149B ASP* 1.3 77.1 + - - +
151B LEU* 3.1 4.6 + - - +
152B GLU* 2.9 41.5 + - - +
160B ALA* 5.1 0.3 - - - +
164B LEU* 3.6 18.0 - - + +
223B ARG* 3.7 14.1 - - - +
215C MET* 3.6 46.2 + - + -
216C MET* 3.5 32.5 - - + +
218C LYS* 6.4 0.2 - - - +
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Residues in contact with ASP 149 (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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145B PHE* 2.8 25.0 + - - +
146B TRP* 3.7 6.8 - - - +
147B LEU 3.2 0.4 - - - -
148B LYS* 1.3 103.2 + - - +
150B THR* 1.3 58.1 + - - +
152B GLU* 3.3 6.8 + - - +
153B ASN* 2.9 37.0 + - - +
220B THR* 3.9 21.4 - - + +
223B ARG* 2.9 31.6 + - - +
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Residues in contact with THR 150 (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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90B TRP* 2.9 30.1 + - - +
94B TYR* 3.8 18.1 - - + -
117B LEU* 3.6 39.9 - - + +
118B THR* 4.6 0.4 - - + +
146B TRP 2.8 20.1 + - - -
147B LEU* 3.2 12.8 + - + -
149B ASP* 1.3 76.1 - - - +
151B LEU* 1.3 59.8 + - - +
153B ASN* 3.2 11.7 + - - +
154B THR* 2.8 27.2 + - - +
220B THR* 4.7 0.6 - - - +
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Residues in contact with LEU 151 (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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117B LEU* 4.0 16.5 - - + +
134B LEU* 4.1 18.2 - - + -
147B LEU 2.9 12.6 + - - +
148B LYS* 3.6 8.1 - - - +
150B THR* 1.3 72.9 - - - +
152B GLU* 1.3 62.7 + - - +
154B THR* 2.9 19.1 + - - -
155B ILE* 2.9 39.6 + - + +
160B ALA* 4.0 16.2 - - + -
163B ALA* 4.2 9.9 - - + -
164B LEU* 3.7 29.6 - - + -
180B ILE* 3.8 28.0 - - + -
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Residues in contact with GLU 152 (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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157A HIS* 5.1 2.3 - - - +
148B LYS* 2.9 28.5 + - - +
149B ASP* 3.3 7.8 + - - +
151B LEU* 1.3 77.4 - - - +
153B ASN* 1.3 61.5 + - - +
154B THR 3.1 0.2 - - - -
156B GLY* 2.8 35.2 + - - -
157B HIS* 2.8 54.1 + - - +
160B ALA* 4.1 6.7 - - + +
216C MET* 3.8 12.9 - - - +
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Residues in contact with ASN 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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157A HIS* 3.1 50.7 + - + +
158A ARG* 3.3 16.5 + - - +
161A GLU* 5.0 2.5 - - - +
94B TYR* 3.0 25.1 + - - +
149B ASP* 2.9 23.1 + - - +
150B THR 3.4 7.0 - - - +
151B LEU 3.2 0.2 - - - -
152B GLU* 1.3 77.6 - - - +
154B THR* 1.3 58.2 + - - +
216B MET 5.1 0.6 + - - -
220B THR* 3.0 27.0 + - - +
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Residues in contact with THR 154 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158A ARG* 3.3 23.3 - - + +
117B LEU* 3.7 35.5 + - + +
122B ARG* 3.7 28.4 + - - +
150B THR* 2.8 18.9 + - - +
151B LEU* 2.9 7.7 + - - -
153B ASN* 1.3 81.9 - - - +
155B ILE* 1.3 66.9 + - + +
179B GLY* 3.8 19.3 - - - +
180B ILE* 4.3 1.3 - - - -
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Residues in contact with ILE 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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151B LEU* 2.9 38.2 + - + +
154B THR* 1.3 82.7 - - + +
156B GLY* 1.3 60.6 + - - +
159B ALA* 3.6 26.4 + - + +
160B ALA* 3.6 25.1 - - - +
163B ALA* 4.3 7.0 - - + -
170B PHE* 5.2 2.5 - - + -
178B VAL* 3.4 34.9 - - + +
179B GLY* 3.5 1.8 - - - -
180B ILE* 3.5 32.8 - - + +
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Residues in contact with GLY 156 (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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152B GLU* 2.8 21.0 + - - -
154B THR 3.8 0.6 - - - -
155B ILE* 1.3 79.8 - - - +
157B HIS* 1.3 67.1 + - - -
158B ARG 3.5 1.8 - - - -
160B ALA* 3.1 24.8 + - - +
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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