Contacts of the helix formed by residues 153 - 167 (chain A) in PDB entry 3GUC
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 THR 153 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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150A ASN* 3.5 17.1 + - - +
151A ILE 3.4 0.3 - - - +
152A THR* 1.3 81.2 + - - +
154A VAL* 1.3 54.4 + - - +
155A GLU* 3.6 13.5 - - + +
156A ASN* 3.4 31.5 + - - +
157A PHE* 2.8 36.6 + - - +
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Residues in contact with VAL 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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152A THR 4.1 1.5 + - - +
153A THR* 1.3 71.2 - - - +
155A GLU* 1.3 64.2 + - - +
157A PHE* 3.3 7.9 + - + +
158A GLN* 3.0 44.1 + - + +
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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
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153A THR* 3.3 10.5 - - + +
154A VAL* 1.3 80.2 - - - +
156A ASN* 1.3 68.9 + - - +
158A GLN* 3.4 22.6 + - - +
159A HIS* 3.5 26.0 + - + +
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Residues in contact with ASN 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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149A TYR* 3.6 28.1 - - + +
150A ASN* 3.1 43.3 + - - +
151A ILE* 4.6 1.6 - - - -
153A THR* 3.3 17.7 + - + +
155A GLU* 1.3 82.1 - - - +
157A PHE* 1.3 59.6 + - - +
159A HIS* 3.2 22.3 + - - +
160A PHE* 2.9 27.8 + - - +
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Residues in contact with PHE 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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151A ILE 3.5 7.8 + - - +
152A THR 5.4 0.2 - - - -
153A THR 2.8 18.3 + - - +
154A VAL* 3.4 9.6 - - + +
156A ASN* 1.3 74.6 - - - +
158A GLN* 1.3 74.8 - - - +
160A PHE* 3.3 11.0 + + - +
161A MET* 2.9 53.3 + - + +
190A THR* 3.4 43.3 - - + -
193A THR* 4.0 17.5 - - + -
194A ALA* 3.6 32.3 - - + -
197A GLU* 4.8 4.3 - - - -
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Residues in contact with GLN 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 VAL* 3.0 44.3 + - + +
155A GLU* 3.4 12.8 - - - +
156A ASN 3.3 0.4 - - - -
157A PHE* 1.3 91.1 - - - +
159A HIS* 1.3 63.4 + - + +
161A MET* 3.5 18.1 + - - +
162A ASP* 3.0 27.2 + - - +
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Residues in contact with HIS 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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149A TYR* 3.4 28.3 - + + +
155A GLU* 3.5 34.6 + - + +
156A ASN* 3.2 23.3 + - - +
158A GLN* 1.3 78.6 - - + +
160A PHE* 1.3 63.5 + - - +
162A ASP* 3.0 11.2 + - - +
163A ARG* 2.9 26.3 + - + +
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Residues in contact with PHE 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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79A VAL* 3.7 30.7 - - + -
103A PHE* 3.6 28.5 - + - -
149A TYR* 3.5 8.0 + - - +
151A ILE* 4.1 24.0 - - + -
156A ASN 2.9 13.0 + - - +
157A PHE* 3.4 20.2 - + - +
158A GLN 3.3 0.2 - - - -
159A HIS* 1.3 76.1 - - - +
161A MET* 1.3 63.6 + - - +
163A ARG* 3.2 2.6 + - - +
164A ILE* 3.0 53.1 + - + +
178A VAL* 4.8 3.4 - - + -
190A THR 5.0 0.2 - - - -
191A ILE* 4.3 26.9 - - + -
194A ALA* 4.0 26.2 - - + -
195A CYS* 6.0 1.6 - - - -
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Residues in contact with MET 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 PHE* 2.9 50.9 + - + +
158A GLN* 3.8 23.8 - - - +
160A PHE* 1.3 72.4 - - - +
162A ASP* 1.3 54.1 + - - +
164A ILE* 3.4 3.6 + - - +
165A SER* 2.7 38.6 + - - +
194A ALA* 3.9 27.4 - - + -
197A GLU* 3.6 38.4 - - - +
198A LEU* 4.0 18.7 - - + +
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Residues in contact with ASP 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 GLN 3.0 15.6 + - - +
159A HIS* 3.0 13.4 + - - +
161A MET* 1.3 74.6 - - - +
163A ARG* 1.3 89.1 + - - +
165A SER* 4.5 0.7 - - - -
166A ASN* 3.0 52.7 + - - +
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Residues in contact with ARG 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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99A LYS* 4.1 0.2 - - - +
101A LEU* 4.0 7.2 - - + +
103A PHE* 4.0 18.8 - - + -
145A GLU* 2.6 43.8 + - - +
147A HIS* 3.6 20.9 - - + +
149A TYR* 4.4 4.5 - - - +
159A HIS* 2.9 19.5 + - + +
160A PHE 3.2 0.6 + - - +
162A ASP* 1.3 97.0 + - - +
164A ILE* 1.3 63.0 + - - +
166A ASN* 4.0 11.7 - - - +
167A GLY* 2.6 46.8 + - - -
171A GLU* 2.8 43.6 + - - -
175A VAL* 4.1 1.0 - - - +
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Residues in contact with ILE 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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77A ALA* 3.8 28.7 - - + -
101A LEU* 5.3 0.2 - - + -
103A PHE* 4.3 6.5 - - + -
160A PHE* 3.0 49.2 + - + +
161A MET* 3.8 4.7 - - - +
163A ARG* 1.3 79.7 - - - +
165A SER* 1.3 56.9 + - - +
174A PRO* 3.5 4.0 - - - +
175A VAL* 3.1 30.0 + - + -
178A VAL* 3.9 11.9 - - + -
194A ALA* 5.9 1.3 - - + -
195A CYS* 5.4 2.9 - - - -
198A LEU* 4.0 17.9 - - + -
200A GLN* 3.8 33.6 + - + +
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Residues in contact with SER 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 MET* 2.7 24.1 + - - +
162A ASP* 4.5 0.3 - - - -
164A ILE* 1.3 75.4 - - - +
166A ASN* 1.3 77.8 + - - +
172A GLY 4.0 1.6 - - - +
173A LYS* 3.2 2.4 - - - -
174A PRO* 3.1 28.4 - - - +
198A LEU* 3.4 26.4 - - - +
200A GLN* 5.9 0.2 - - - +
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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 ASP* 3.0 39.2 + - - +
163A ARG* 4.0 11.4 - - - +
165A SER* 1.3 92.6 - - - +
167A GLY* 1.3 57.2 + - - +
168A GLY 3.2 8.6 + - - -
171A GLU* 3.4 14.2 - - - +
172A GLY* 2.9 44.5 + - - +
173A LYS 3.3 3.8 - - - -
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Residues in contact with GLY 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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99A LYS* 2.6 25.3 + - - +
101A LEU* 3.5 14.9 - - - +
163A ARG* 2.6 50.3 + - - +
164A ILE 4.5 0.2 - - - -
166A ASN* 1.3 70.4 - - - +
168A GLY* 1.3 62.3 + - - +
171A GLU* 4.3 0.2 - - - -
175A VAL* 4.0 4.7 - - - -
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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