Contacts of the helix formed by residues 145 - 159 (chain C) in PDB entry 4GUP
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 ALA 145 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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72C MET* 6.5 0.4 - - + -
143C TRP 3.3 1.2 + - - -
144C GLU* 1.4 74.8 - - + +
146C ASN* 1.3 68.2 + - - +
147C GLN 3.3 2.7 + - - -
148C HIS* 3.4 33.6 + - + +
149C GLU* 3.7 4.4 + - - +
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Residues in contact with ASN 146 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140C LYS 4.3 2.3 - - - +
141C GLN 3.6 8.9 + - - +
142C ALA* 3.3 20.6 + - - +
143C TRP* 2.7 60.8 + - - +
144C GLU 3.4 0.2 - - - -
145C ALA* 1.3 76.0 - - - +
147C GLN* 1.3 63.5 + - + +
149C GLU* 3.6 5.5 + - - +
150C LEU* 3.5 28.7 + - + +
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Residues in contact with GLN 147 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127C LEU* 5.5 0.3 - - - +
145C ALA 3.3 1.4 + - - -
146C ASN* 1.3 76.7 - - + +
148C HIS* 1.3 61.0 + - - +
150C LEU* 3.2 11.6 + - - +
151C LEU* 3.0 37.2 + - + +
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Residues in contact with HIS 148 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72C MET* 5.8 8.5 - - + -
145C ALA* 3.4 24.6 + - + +
146C ASN 3.5 0.6 - - - -
147C GLN* 1.3 76.1 - - - +
149C GLU* 1.4 82.3 + - + +
151C LEU* 3.4 9.1 + - - +
152C TYR* 2.8 53.1 + + + +
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Residues in contact with GLU 149 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9C ARG* 5.5 3.6 + - - -
72C MET* 5.4 11.1 - - - +
76C GLU* 5.3 0.7 - - - +
94C ARG* 4.9 3.3 + - - -
112C TYR* 4.6 8.9 + - - -
129C TRP* 6.3 0.9 - - + -
143C TRP* 3.7 39.4 - - + +
144C GLU 5.2 3.5 - - - +
145C ALA 4.1 4.5 - - - +
146C ASN* 3.6 10.0 + - - +
147C GLN 3.2 0.2 - - - -
148C HIS* 1.4 95.4 + - + +
150C LEU* 1.4 59.6 + - + +
152C TYR* 3.0 7.5 + - - +
153C GLN* 2.8 56.0 + - + +
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Residues in contact with LEU 150 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122C PHE* 3.8 8.6 - - + -
127C LEU* 3.4 50.0 - - + +
129C TRP* 3.4 36.3 - - + +
143C TRP* 4.2 14.1 - - + +
146C ASN* 3.5 20.4 + - + +
147C GLN* 3.2 10.5 + - - +
149C GLU* 1.4 79.7 - - + +
151C LEU* 1.3 55.7 + - - +
153C GLN* 3.5 6.2 + - - +
154C LYS* 2.9 29.1 + - - +
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Residues in contact with LEU 151 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127C LEU* 3.9 23.3 - - + -
147C GLN* 3.0 24.1 + - + +
148C HIS* 3.7 7.4 - - - +
150C LEU* 1.3 73.3 - - - +
152C TYR* 1.4 57.8 + - - +
154C LYS* 3.3 16.1 + - + +
155C ASN* 2.9 34.4 + - - +
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Residues in contact with TYR 152 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62C TYR* 5.0 2.4 - - - -
65C LEU* 3.8 18.8 - - + +
69C TRP* 3.4 29.3 - + - -
148C HIS* 2.8 38.0 + + + +
149C GLU* 3.3 8.1 - - - +
151C LEU* 1.4 71.3 - - - +
153C GLN* 1.3 83.1 + - - +
155C ASN* 3.7 8.9 + - - +
156C TRP* 3.0 38.3 + + + +
301C 6FP 4.1 14.0 + - - -
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Residues in contact with GLN 153 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9C ARG* 5.3 0.3 + - - -
94C ARG* 2.9 26.8 + - - +
96C ILE* 4.7 5.8 - - + +
110C LEU* 3.6 28.3 - - + -
122C PHE* 4.3 11.9 - - + -
149C GLU* 2.8 47.1 + - + +
150C LEU* 3.7 5.6 - - - +
152C TYR* 1.3 87.3 - - - +
154C LYS* 1.4 67.0 + - - +
156C TRP* 3.0 16.8 + - + +
157C LEU* 3.1 19.2 + - + +
301C 6FP 3.1 21.3 + - - -
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Residues in contact with LYS 154 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122C PHE* 4.1 11.0 - - + -
124C LYS* 2.7 33.8 + - + +
125C ASP* 4.1 11.3 + - - +
127C LEU* 3.8 21.9 - - + +
150C LEU 2.9 21.5 + - - +
151C LEU* 3.6 16.2 - - + +
153C GLN* 1.4 72.4 - - - +
155C ASN* 1.4 57.1 + - - +
157C LEU* 3.3 5.8 + - - +
158C GLU* 3.0 66.0 + - + +
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Residues in contact with ASN 155 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151C LEU 2.9 20.3 + - - +
152C TYR* 4.0 7.8 + - - +
154C LYS* 1.4 71.4 - - - +
156C TRP* 1.4 66.0 + - - +
158C GLU* 4.2 7.9 - - - -
159C GLU* 2.8 51.3 + - + +
160C GLU* 3.7 13.2 + - - +
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Residues in contact with TRP 156 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5C LEU* 4.7 4.5 - - + -
7C TYR* 4.0 25.6 - + - -
62C TYR* 4.8 1.0 + - - -
96C ILE* 3.7 34.3 - - + -
97C GLY* 3.9 14.6 - - - -
152C TYR* 3.0 28.0 + + + +
153C GLN* 3.0 6.7 + - - +
155C ASN* 1.4 80.4 - - - +
157C LEU* 1.4 71.7 + - + +
160C GLU* 3.3 44.7 + - + +
161C CYS* 2.6 70.7 + - + +
164C TRP* 4.5 8.1 - + - -
301C 6FP 4.1 31.0 + - - +
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Residues in contact with LEU 157 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96C ILE* 4.1 12.3 - - + -
97C GLY 3.7 9.6 - - - +
98C CYS* 5.2 5.1 - - + +
108C GLY* 4.0 8.9 - - - +
109C PHE 3.2 41.3 - - - +
110C LEU* 4.8 4.0 - - + -
122C PHE* 4.1 28.5 - - + -
124C LYS* 4.4 21.3 - - + -
153C GLN* 3.1 20.0 + - + +
154C LYS 3.7 4.3 - - - +
156C TRP* 1.4 90.3 - - + +
158C GLU* 1.4 61.5 - - - +
159C GLU 3.3 3.8 + - - +
161C CYS* 3.8 13.5 - - - +
162C ILE* 4.5 4.9 + - - +
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Residues in contact with GLU 158 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124C LYS* 3.4 32.3 + - - +
125C ASP* 5.2 0.7 - - - +
154C LYS* 3.0 55.8 + - - +
155C ASN* 4.0 6.6 - - - +
157C LEU* 1.4 75.5 - - - +
159C GLU* 1.4 75.9 + - + +
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Residues in contact with GLU 159 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155C ASN* 2.8 40.1 + - + +
157C LEU 4.0 0.5 - - - +
158C GLU* 1.4 100.3 - - + +
160C GLU* 1.3 68.1 + - + +
161C CYS 2.9 4.9 + - - -
162C ILE* 3.2 16.3 + - - +
163C ALA* 3.7 9.7 + - - +
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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