Contacts of the helix formed by residues 153 - 172 (chain A) in PDB entry 3C6G
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 153 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151A GLN* 3.2 9.7 + - - +
152A LYS* 1.3 75.9 - - - +
154A PHE* 1.3 60.0 + - - +
155A GLU 3.5 1.1 - - - -
156A SER* 2.6 29.0 + - - -
157A LYS* 3.2 33.7 + - - +
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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
----------------------------------------------------------
147A PHE 4.2 7.9 - - - -
148A GLY* 3.1 43.7 - - - +
149A TYR* 3.7 11.0 - - + -
151A GLN* 3.1 13.5 + - + +
152A LYS 3.2 0.2 - - - -
153A SER* 1.3 76.3 + - - +
155A GLU* 1.3 68.0 + - - +
157A LYS* 2.9 31.7 + - + +
158A ILE* 3.2 26.8 + - + +
190A ILE* 3.9 20.6 - - + -
193A LEU* 4.6 19.7 - - + -
194A ILE* 3.9 21.5 - - + -
453A LEU* 3.7 20.9 - - + -
456A MET* 4.7 6.3 - - + -
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Residues in contact with GLU 155 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151A GLN 4.6 0.6 + - - -
152A LYS 4.2 7.0 + - - +
153A SER 3.5 0.2 - - - -
154A PHE* 1.3 79.9 - - - +
156A SER* 1.3 57.5 + - - +
158A ILE* 3.2 12.3 + - - +
159A LEU* 3.0 33.8 + - + +
350A PRO 4.3 2.8 - - - +
351A SER* 3.3 19.1 + - - -
352A TRP* 3.0 40.7 + - - +
353A ASP* 4.9 4.5 + - - +
456A MET* 4.3 12.2 - - + +
460A LEU* 4.0 18.4 - - + -
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Residues in contact with SER 156 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152A LYS 5.0 0.8 + - - -
153A SER* 2.6 29.9 + - - -
155A GLU* 1.3 75.7 - - - +
157A LYS* 1.3 56.3 + - - +
159A LEU* 3.5 13.0 - - - +
160A GLU* 2.7 43.3 + - - +
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Residues in contact with LYS 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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147A PHE 5.7 1.2 + - - -
151A GLN* 3.9 13.7 + - - -
153A SER* 3.2 38.5 + - - +
154A PHE* 2.9 23.8 + - + +
156A SER* 1.3 76.4 + - - +
158A ILE* 1.3 65.5 + - - +
160A GLU* 3.3 19.7 + - - +
161A GLU* 3.1 21.7 + - - +
190A ILE* 4.5 1.4 - - - +
193A LEU* 3.9 35.8 - - + +
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Residues in contact with ILE 158 (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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154A PHE* 3.2 36.6 + - + +
155A GLU* 3.2 8.7 + - - +
157A LYS* 1.3 76.1 - - - +
159A LEU* 1.3 58.2 + - - +
161A GLU* 2.9 20.4 + - - +
162A THR* 2.9 13.4 + - + +
190A ILE* 4.1 32.1 - - + -
453A LEU* 5.0 1.3 - - + -
456A MET* 4.2 27.6 - - + -
457A GLU* 4.5 9.6 - - + +
460A LEU* 3.7 30.7 - - + -
461A PHE* 4.6 13.7 - - + -
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Residues in contact with LEU 159 (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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155A GLU* 3.0 28.8 + - + +
156A SER* 3.7 14.4 - - - +
157A LYS 3.3 0.4 - - - -
158A ILE* 1.3 75.6 - - - +
160A GLU* 1.3 61.3 - - - +
162A THR* 2.7 32.4 + - + +
163A LYS* 3.2 9.9 + - - +
349A LYS* 4.7 24.9 - - + +
350A PRO* 3.2 54.7 - - + +
460A LEU* 4.7 11.4 - - + -
464A ALA* 5.3 0.4 - - + -
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Residues in contact with GLU 160 (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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156A SER* 2.7 28.1 + - - +
157A LYS* 3.5 23.1 - - - +
158A ILE 3.1 0.2 - - - -
159A LEU* 1.3 73.7 - - - +
161A GLU* 1.3 62.5 + - - +
163A LYS* 3.2 16.4 + - - +
164A PHE* 3.3 28.8 + - + -
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Residues in contact with GLU 161 (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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157A LYS 3.1 11.1 + - - +
158A ILE 2.9 9.3 + - - +
160A GLU* 1.3 74.5 - - - +
162A THR* 1.3 65.9 + - - +
164A PHE* 3.3 4.6 + - - +
165A PHE* 3.0 24.0 + - - +
186A ALA* 3.5 22.1 - - - +
189A ASN* 3.3 17.7 + - - +
190A ILE* 3.7 16.1 - - + +
193A LEU* 5.7 1.9 - - - +
199A ARG* 2.8 44.7 + - - +
202A TYR* 2.5 28.2 + - - -
461A PHE* 3.9 8.7 - - + -
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Residues in contact with THR 162 (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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158A ILE* 2.9 20.3 + - + +
159A LEU* 2.7 35.2 + - + +
161A GLU* 1.3 74.8 - - - +
163A LYS* 1.3 52.6 + - - +
165A PHE* 3.5 2.4 - - - +
166A ASN* 2.7 40.3 + - - +
460A LEU* 3.8 22.2 - - + +
461A PHE* 3.6 34.1 - - + -
464A ALA* 3.7 18.3 - - + +
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Residues in contact with LYS 163 (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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159A LEU 3.2 8.1 + - - +
160A GLU* 3.4 11.4 - - - +
161A GLU 3.1 0.8 - - - -
162A THR* 1.3 78.9 + - - +
164A PHE* 1.3 59.6 + - + +
166A ASN* 4.7 3.6 - - - +
167A ASP* 2.8 58.2 + - - +
468A ARG* 5.1 3.8 - - - +
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Residues in contact with PHE 164 (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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160A GLU* 3.3 33.0 + - + -
161A GLU* 3.3 6.0 + - - +
163A LYS* 1.3 77.9 - - - +
165A PHE* 1.3 57.6 + - - +
167A ASP* 3.7 7.4 - - - +
168A ALA* 2.9 30.5 + - - +
199A ARG* 3.5 49.4 - - - -
202A TYR* 3.6 23.3 - + + +
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Residues in contact with PHE 165 (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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161A GLU 3.0 17.9 + - - +
162A THR* 3.5 7.0 - - - +
164A PHE* 1.3 76.0 - - - +
166A ASN* 1.3 75.3 + - - +
168A ALA* 3.1 6.6 + - - +
169A ILE* 3.0 51.2 + - + +
179A PHE* 4.3 8.7 - + - -
182A LEU* 3.8 26.5 - - + -
183A ILE* 3.7 43.1 - - + -
186A ALA* 4.0 4.7 - - + -
202A TYR* 3.5 12.5 + + - +
319A LEU* 6.3 1.1 - - + -
461A PHE* 3.9 29.8 - + + -
464A ALA* 6.4 0.2 - - + -
465A LEU* 4.2 17.7 - - + -
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Residues in contact with ASN 166 (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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162A THR 2.7 24.0 + - - +
163A LYS* 4.1 1.3 - - - +
165A PHE* 1.3 88.1 - - - +
167A ASP* 1.3 61.5 + - - +
169A ILE* 3.1 15.7 + - - +
170A GLU* 3.0 20.3 + - - +
464A ALA* 3.1 37.1 + - - +
465A LEU* 3.8 12.1 + - - +
468A ARG* 3.3 32.7 + - - +
469A PHE* 3.6 13.7 - - + -
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Residues in contact with ASP 167 (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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163A LYS* 2.8 49.2 + - - +
164A PHE* 3.7 7.8 + - + +
166A ASN* 1.3 71.9 - - - +
168A ALA* 1.3 60.9 + - - +
170A GLU* 3.1 14.4 + - - +
171A THR* 3.2 13.2 + - - -
468A ARG* 3.0 29.9 + - - +
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Residues in contact with ALA 168 (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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164A PHE 2.9 15.3 + - - +
165A PHE 3.3 9.9 - - - +
167A ASP* 1.3 75.8 - - - +
169A ILE* 1.3 62.9 + - - +
171A THR* 3.1 24.4 - - - +
172A TYR* 3.7 11.6 - - - -
182A LEU* 3.6 29.2 - - + -
202A TYR* 4.3 9.6 - - + -
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Residues in contact with ILE 169 (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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165A PHE* 3.0 57.5 + - + +
166A ASN* 3.1 12.3 + - - +
168A ALA* 1.3 76.3 - - - +
170A GLU* 1.3 63.1 + - - +
172A TYR* 3.2 19.4 + - - +
173A LYS 4.3 1.4 + - - -
174A GLY 5.3 0.2 + - - -
177A PHE* 4.2 9.9 - - + -
179A PHE* 4.1 16.4 - - + -
182A LEU* 4.1 12.6 - - + -
465A LEU* 3.5 16.6 - - + -
469A PHE* 3.5 15.4 - - + -
498A ALA* 3.5 35.0 - - + +
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Residues in contact with GLU 170 (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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166A ASN 3.0 5.8 + - - +
167A ASP* 3.1 11.0 + - - +
169A ILE* 1.3 73.6 - - - +
171A THR* 1.3 65.4 + - - +
173A LYS* 2.8 51.5 + - - +
174A GLY 6.1 0.2 - - - +
468A ARG* 3.6 29.2 + - - +
469A PHE* 4.0 18.9 - - + -
500A ARG* 4.2 27.5 + - - +
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Residues in contact with THR 171 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167A ASP 3.2 11.2 + - - -
168A ALA* 3.1 22.3 + - - +
170A GLU* 1.3 75.1 - - - +
172A TYR* 1.3 76.1 + - + +
173A LYS* 3.3 14.6 + - - +
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Residues in contact with TYR 172 (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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168A ALA 3.7 17.9 - - - -
169A ILE 3.2 10.2 + - - +
170A GLU 2.9 1.6 + - - -
171A THR* 1.3 88.2 - - + +
173A LYS* 1.3 71.6 + - - +
174A GLY* 3.3 1.6 - - - +
175A ARG* 3.1 38.6 + - + +
176A PRO 5.0 1.6 - - - -
177A PHE* 3.5 58.6 - + + +
178A ASP 5.4 0.2 + - - -
182A LEU* 4.7 7.9 - - + +
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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
------------------------------------------------------------
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