Contacts of the helix formed by residues 159 - 169 (chain C) in PDB entry 1RRP
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 LYS 159 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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147C TYR* 3.5 36.2 + - + +
156C ASN* 3.4 46.9 + - - +
158C GLU* 1.3 90.8 + - - +
160C PRO* 1.3 64.7 - - + +
162C LEU* 4.2 9.9 - - + -
163C TRP* 2.8 26.2 + - - +
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Residues in contact with PRO 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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26C PHE* 4.2 8.3 - - + -
87C ILE* 4.2 19.1 - - + -
118C VAL* 3.8 25.7 - - + +
120C CYS* 4.0 9.2 - - - -
147C TYR* 4.3 2.9 - - + -
149C ILE* 3.9 20.2 - - + -
156C ASN 3.0 14.1 - - - +
157C PHE 3.5 11.0 - - - +
158C GLU 2.9 7.4 - - - +
159C LYS* 1.3 93.9 - - + +
161C PHE* 1.3 61.5 + - + +
163C TRP* 3.4 2.6 + - - +
164C LEU* 3.2 28.4 + - - +
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Residues in contact with PHE 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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13C LEU* 3.6 28.9 - - + -
26C PHE* 3.8 24.0 - + - -
27C VAL* 5.5 3.1 - - + -
30C HIS* 3.0 35.0 - + - -
50C LEU* 3.2 29.4 - - + -
52C PHE* 3.3 35.7 - + + -
61C PHE* 3.7 20.8 - + + -
63C VAL* 4.6 1.8 - - + -
87C ILE* 4.1 4.7 - - + -
157C PHE 3.7 9.4 - - - -
158C GLU* 2.9 7.6 + - - +
160C PRO* 1.3 72.1 - - - +
162C LEU* 1.3 58.8 + - - +
164C LEU* 3.1 7.3 + - + +
165C ALA* 2.7 34.8 + - - +
176C PHE* 3.8 3.1 - - + -
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Residues in contact with LEU 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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158C GLU* 2.9 16.8 + - + +
159C LYS* 3.8 9.6 - - + +
161C PHE* 1.3 79.7 - - - +
163C TRP* 1.3 65.7 + - - +
165C ALA* 3.2 1.0 + - + +
166C ARG* 3.0 74.7 + - + +
174C LEU* 3.9 9.0 - - + +
175C GLU* 4.5 2.0 - - + -
176C PHE* 3.1 49.2 - - + +
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Residues in contact with TRP 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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116C PRO* 4.0 11.7 - - + -
117C ILE 3.8 20.6 - - - -
118C VAL* 3.3 17.5 - - + -
143C ASN 5.9 1.1 - - - -
144C LEU* 5.8 1.1 - - + -
145C GLN* 3.3 38.3 + - + -
147C TYR* 3.4 23.3 - - + +
159C LYS 2.8 23.2 + - - +
160C PRO 3.5 3.1 - - - +
162C LEU* 1.3 75.8 - - - +
164C LEU* 1.3 87.4 + - + +
166C ARG* 3.4 12.9 - - - +
167C LYS* 3.3 55.5 + - + +
18D PHE* 4.7 7.9 - + - -
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Residues in contact with LEU 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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13C LEU* 3.9 26.7 - - + -
61C PHE* 4.2 7.4 - - + -
85C CYS* 3.8 13.5 - - + -
86C ALA 4.8 1.1 - - - +
87C ILE* 4.3 11.4 - - + -
116C PRO* 3.3 38.6 - - + +
117C ILE* 4.3 1.8 - - - +
118C VAL* 4.0 9.2 - - + -
160C PRO 3.4 20.9 - - - +
161C PHE* 3.1 9.5 + - - +
163C TRP* 1.3 90.7 - - + +
165C ALA* 1.3 69.1 + - - +
167C LYS* 2.7 14.7 + - - -
168C LEU* 2.7 23.5 + - + +
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Residues in contact with ALA 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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11C PHE* 5.2 1.8 - - - -
59C ILE* 3.8 27.8 - - + -
61C PHE* 4.1 9.9 - - + -
161C PHE 2.7 16.7 + - - +
162C LEU 3.3 10.1 - - - +
164C LEU* 1.3 73.3 - - - +
166C ARG* 1.3 67.1 + - + +
168C LEU* 2.8 6.4 + - - +
169C ILE* 2.8 28.8 + - - +
174C LEU* 4.6 8.1 - - + -
176C PHE* 4.1 11.7 - - + -
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Residues in contact with ARG 166 (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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162C LEU* 3.0 59.3 - - + +
163C TRP* 3.4 12.1 - - + +
165C ALA* 1.3 74.1 - - - +
167C LYS* 1.3 66.9 + - + +
170C GLY* 2.8 27.9 + - - -
171C ASP 3.7 19.2 + - - +
172C PRO* 3.0 35.7 + - + -
173C ASN* 4.7 2.2 - - - +
174C LEU* 3.3 21.7 + - + +
175C GLU* 5.0 3.6 - - - +
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Residues in contact with LYS 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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116C PRO* 4.2 16.8 - - + -
163C TRP* 3.3 60.9 + - + +
164C LEU 2.7 13.3 + - - +
166C ARG* 1.3 79.3 - - - +
168C LEU* 1.3 63.9 + - - +
170C GLY* 4.1 4.5 + - - -
17D HIS* 5.2 13.1 - - - +
18D PHE* 4.5 27.0 - - + +
19D GLU 4.8 3.1 - - - +
20D PRO* 4.3 9.4 - - - +
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Residues in contact with LEU 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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11C PHE* 3.5 41.3 - - + -
61C PHE* 5.1 0.9 - - + -
84C GLN* 4.1 22.9 - - + +
85C CYS* 4.4 5.6 - - + -
116C PRO* 3.9 23.8 - - + -
164C LEU* 2.7 46.6 + - + +
165C ALA* 2.8 6.5 + - - +
167C LYS* 1.3 70.6 - - - +
169C ILE* 1.3 58.3 + - - +
19D GLU 5.4 0.9 - - - +
20D PRO* 2.9 30.8 - - - +
21D VAL* 3.1 34.2 + - + -
22D VAL* 5.2 0.2 - - - -
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Residues in contact with ILE 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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9C VAL* 4.4 9.9 - - + -
11C PHE* 4.1 14.8 - - + -
56C ARG* 4.5 0.9 - - + -
59C ILE* 4.8 6.7 - - + -
165C ALA* 2.8 21.0 + - - +
166C ARG 4.1 0.7 - - - +
168C LEU* 1.3 72.2 - - - +
170C GLY* 1.3 59.4 + - - +
171C ASP* 3.9 6.7 - - + +
174C LEU* 3.7 26.5 - - + -
20D PRO* 2.9 22.0 - - - +
22D VAL* 3.5 31.6 - - + +
24D LEU* 3.4 37.4 - - + +
25D PRO* 4.0 16.2 - - + -
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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