Contacts of the helix formed by residues 159 - 170 (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 GLU 159 (chain C).
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Specific contacts
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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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Residues in contact with GLU 160 (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* 3.3 20.8 + - - -
155C ASN* 4.4 13.1 + - - +
156C TRP* 3.3 37.6 + - + +
159C GLU* 1.3 78.6 - - + +
161C CYS* 1.3 61.7 + - - +
163C ALA* 3.5 7.7 + - - +
164C TRP* 3.1 50.6 + - + +
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Residues in contact with CYS 161 (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* 3.8 10.0 - - - +
97C GLY* 4.1 1.1 - - - -
98C CYS* 2.7 45.8 - - - -
156C TRP* 2.6 61.6 + - + +
157C LEU* 3.8 10.8 - - - +
159C GLU 2.9 4.2 + - - -
160C GLU* 1.3 71.1 - - - +
162C ILE* 1.4 60.9 + - - +
164C TRP* 3.5 3.3 + - - +
165C LEU* 3.1 20.4 + - - +
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Residues in contact with ILE 162 (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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98C CYS* 3.3 30.7 - - + -
99C GLU 3.4 23.6 - - - +
100C LEU* 3.9 20.2 - - + -
106C THR* 3.5 27.6 - - + +
107C THR 4.3 1.8 - - - +
157C LEU 4.5 4.8 + - - +
159C GLU 3.2 8.8 + - - +
161C CYS* 1.4 76.3 - - - +
163C ALA* 1.3 68.7 + - - +
165C LEU* 3.4 7.5 + - + +
166C LYS* 3.1 45.5 + - - +
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Residues in contact with ALA 163 (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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159C GLU 3.7 9.2 + - - +
160C GLU* 3.5 13.2 + - - +
162C ILE* 1.3 82.5 - - - +
164C TRP* 1.4 61.1 + - + +
166C LYS* 3.3 13.8 + - - +
167C ARG* 3.2 24.8 + - - +
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Residues in contact with TRP 164 (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* 4.0 12.8 - - + -
7C TYR* 5.8 1.8 - - - -
54C LEU* 4.1 11.7 - - + -
58C HIS* 3.5 36.3 - + - -
61C ARG* 5.4 3.8 - - - -
62C TYR* 4.3 8.9 + + - -
156C TRP* 4.5 8.7 - + - -
160C GLU* 3.1 57.2 + - + +
161C CYS* 3.7 4.9 - - - +
163C ALA* 1.4 72.7 - - + +
165C LEU* 1.3 60.8 + - - +
167C ARG* 3.3 48.9 + - + +
168C PHE* 3.0 58.4 + + + -
171C TYR* 6.2 0.4 - + - -
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Residues in contact with LEU 165 (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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3C HIS 4.1 10.1 - - - +
4C SER* 3.6 34.3 - - - +
5C LEU* 3.7 17.9 - - + +
28C VAL* 4.0 17.3 - - + -
98C CYS* 4.9 2.7 - - - +
99C GLU 4.7 1.6 - - - -
100C LEU* 3.9 37.9 - - + +
161C CYS 3.1 14.1 + - - +
162C ILE* 3.6 15.3 - - + +
163C ALA 3.4 0.2 - - - -
164C TRP* 1.3 74.5 - - - +
166C LYS* 1.3 51.9 + - - +
168C PHE* 3.2 7.2 + - - +
169C LEU* 2.9 48.7 + - + +
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Residues in contact with LYS 166 (chain C).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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100C LEU* 3.8 30.2 - - + +
162C ILE* 3.1 31.8 + - + +
163C ALA* 3.3 12.3 + - - +
165C LEU* 1.3 75.5 - - - +
167C ARG* 1.3 60.6 + - - +
169C LEU* 3.5 11.1 + - + +
170C GLU* 3.2 21.7 + - - +
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Residues in contact with ARG 167 (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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53C ASN 5.7 1.6 + - - -
54C LEU* 4.6 8.7 - - - +
163C ALA 3.2 14.6 + - - +
164C TRP* 3.5 50.9 - - + +
165C LEU 3.3 0.2 - - - -
166C LYS* 1.3 74.3 - - - +
168C PHE* 1.4 60.1 + - + +
170C GLU* 3.0 19.4 + - - +
171C TYR* 3.4 47.8 + - + +
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Residues in contact with PHE 168 (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* 4.0 18.4 - - + -
7C TYR* 3.6 24.7 - - - -
28C VAL* 3.7 33.2 - - + -
33C ILE* 4.4 5.6 - - + -
34C THR* 6.0 0.2 - - + -
49C TRP* 3.9 13.0 - - + -
50C MET* 3.7 36.1 - - + -
54C LEU* 4.0 13.0 - - + -
58C HIS* 5.0 5.4 - + - -
164C TRP* 3.0 48.6 + + + -
165C LEU* 3.2 6.9 + - - +
167C ARG* 1.4 74.4 - - - +
169C LEU* 1.3 56.7 + - - +
171C TYR* 3.1 36.8 + + - +
172C GLY* 3.8 1.2 + - - -
175C THR* 4.7 1.0 + - - -
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Residues in contact with LEU 169 (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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3C HIS* 3.5 53.4 - - + +
28C VAL* 4.5 6.7 - - + -
100C LEU* 5.6 5.2 - - + -
165C LEU* 2.9 43.9 + - + +
166C LYS* 3.8 10.3 - - + +
167C ARG 3.2 0.2 - - - -
168C PHE* 1.3 72.7 - - - +
170C GLU* 1.4 56.3 + - - +
171C TYR 3.1 4.7 - - - -
172C GLY* 3.2 17.3 + - - +
175C THR* 4.3 18.2 - - - -
176C LEU* 3.3 32.4 - - + +
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Residues in contact with GLU 170 (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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166C LYS 3.2 10.3 + - - +
167C ARG* 3.0 13.2 + - - +
169C LEU* 1.4 74.9 - - - +
171C TYR* 1.3 68.5 + - + +
172C GLY 3.3 6.2 + - - +
176C LEU* 3.5 24.0 - - - +
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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