Contacts of the helix formed by residues 152 - 163 (chain A) in PDB entry 1RP1
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 152 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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76A GLY* 3.7 6.7 - - - -
77A PHE 3.3 12.1 + - - -
150A GLY 4.1 0.6 + - - -
151A HIS* 1.3 86.6 - - - +
153A LEU* 1.3 70.7 + - - +
155A ALA* 3.0 19.4 + - - +
156A HIS* 4.0 0.9 + - - -
175A LEU 2.9 15.2 + - - -
176A ASP 3.4 15.2 - - - -
178A VAL* 3.6 20.4 + - - +
252A TRP* 3.6 4.9 - - - -
263A HIS* 2.7 31.5 + - - -
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Residues in contact with LEU 153 (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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76A GLY* 4.1 5.6 - - - -
106A TRP* 4.1 17.5 - - + -
110A SER* 5.0 0.2 - - - -
114A TYR* 3.9 13.7 - - + +
117A ALA* 3.8 25.4 - - + -
118A ALA* 4.1 5.4 - - - -
121A VAL* 3.7 20.8 - - + +
152A SER* 1.3 79.9 + - - +
154A GLY* 1.3 57.1 + - - +
156A HIS* 2.8 23.6 + - - +
157A VAL* 3.1 13.8 + - - +
178A VAL* 3.4 24.9 - - + +
182A PHE* 3.7 20.9 - - + -
252A TRP* 3.4 33.7 - - + -
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Residues in contact with GLY 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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74A ILE* 3.7 9.0 - - - +
75A HIS 3.1 25.5 + - - -
150A GLY* 3.5 14.0 - - - -
151A HIS 2.8 9.6 + - - -
153A LEU* 1.3 77.5 - - - +
155A ALA* 1.3 55.5 + - - +
157A VAL* 3.2 14.1 + - - +
158A ALA* 2.9 24.6 + - - +
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Residues in contact with ALA 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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150A GLY* 3.4 26.2 - - - +
152A SER 3.0 15.6 + - - +
154A GLY* 1.3 77.1 - - - +
156A HIS* 1.3 60.1 + - + +
158A ALA* 3.6 5.2 + - - +
159A GLY 3.0 18.9 + - - -
174A GLY* 4.1 0.9 - - - -
177A PRO* 3.8 32.8 - - + -
191A LEU* 3.4 21.9 - - + +
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Residues in contact with HIS 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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121A VAL* 3.7 5.4 - - + -
152A SER 4.1 4.3 - - - -
153A LEU* 2.8 8.4 + - - +
155A ALA* 1.3 75.4 - - - +
157A VAL* 1.3 61.4 + - - +
158A ALA 3.2 0.2 - - - -
159A GLY* 3.6 1.4 - - - +
160A GLU* 2.9 32.4 + - - +
177A PRO* 4.0 4.7 - - + +
178A VAL* 2.8 52.7 + - + -
182A PHE* 3.5 47.5 - + + -
189A VAL 4.5 4.1 - - - +
190A ARG* 3.7 4.6 - - + -
191A LEU* 3.3 21.2 + - + +
221A MET* 3.6 30.3 - - + -
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Residues in contact with VAL 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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74A ILE* 3.7 18.6 - - + -
106A TRP* 3.8 25.4 - - + +
121A VAL* 3.6 26.4 - - + +
124A VAL* 3.6 26.2 - - + +
125A GLY* 3.4 14.4 - - - +
128A VAL* 4.4 3.6 - - + -
153A LEU 3.1 13.9 + - - +
154A GLY* 3.3 16.4 - - - +
156A HIS* 1.3 75.8 - - - +
158A ALA* 1.3 61.7 + - - +
160A GLU* 3.2 6.2 + - - +
161A ALA* 3.1 18.8 + - - +
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Residues in contact with ALA 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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74A ILE* 4.2 8.9 - - + +
148A LEU* 3.7 32.0 - - + +
150A GLY* 4.6 5.8 - - - +
154A GLY 2.9 16.1 + - - +
155A ALA* 3.6 8.3 - - - +
157A VAL* 1.3 73.8 - - - +
159A GLY* 1.3 59.3 + - - +
161A ALA* 3.2 3.4 + - - +
162A GLY 2.9 26.2 + - - -
172A ILE* 3.4 24.4 - - + +
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Residues in contact with GLY 159 (chain A).
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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155A ALA 3.0 14.1 + - - -
156A HIS 3.3 5.1 + - - -
158A ALA* 1.3 76.0 - - - +
160A GLU* 1.3 49.6 + - - +
162A GLY 3.2 1.2 + - - -
163A SER* 2.8 31.9 + - - -
172A ILE* 4.1 0.4 - - - +
188A GLU 6.0 0.7 - - - -
190A ARG 5.2 1.3 - - - -
191A LEU* 4.0 14.8 - - - +
195A ASP* 3.2 31.3 - - - +
501A CA 4.7 2.2 - - - -
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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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17A TRP* 3.7 20.1 - - - -
121A VAL* 4.3 8.1 - - + +
122A ARG* 3.6 38.8 - - - +
125A GLY* 3.8 14.1 - - - -
156A HIS 2.9 15.5 + - - +
157A VAL 3.4 9.0 - - - +
159A GLY* 1.3 74.2 - - - +
161A ALA* 1.3 63.6 + - - +
163A SER* 3.1 11.4 + - - -
164A ARG* 3.0 55.6 + - - +
188A GLU* 3.9 15.0 - - - +
189A VAL 4.8 6.4 - - - +
190A ARG 5.8 0.2 - - - -
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Residues in contact with ALA 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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125A GLY 3.4 21.8 + - - +
128A VAL* 3.5 19.7 - - + -
129A ALA* 4.1 7.0 - - - +
132A LEU* 4.8 1.6 - - + -
148A LEU* 3.5 25.4 - - + -
157A VAL 3.1 8.7 + - - +
158A ALA* 3.5 2.7 - - - +
160A GLU* 1.3 78.7 - - - +
162A GLY* 1.3 56.2 + - - +
164A ARG* 3.2 3.5 + - - +
165A THR* 2.8 35.1 + - - -
169A LEU* 4.9 0.2 - - - -
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Residues in contact with GLY 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 ALA 2.9 12.5 + - - -
159A GLY 3.6 2.9 - - - -
161A ALA* 1.3 73.1 - - - +
163A SER* 1.3 67.3 + - - +
165A THR* 3.0 22.9 + - - +
166A PRO* 4.8 0.9 - - - +
169A LEU* 3.7 16.7 - - - +
172A ILE* 4.2 0.4 - - - -
194A THR 5.3 0.7 - - - +
195A ASP* 3.1 28.2 - - - +
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Residues in contact with SER 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 GLY 2.8 16.8 + - - -
160A GLU* 3.1 17.9 + - - -
162A GLY* 1.3 72.7 - - - +
164A ARG* 1.3 62.8 + - - +
165A THR 3.7 0.7 + - - -
166A PRO* 5.1 3.5 - - - +
188A GLU* 4.8 21.9 + - - +
194A THR 5.6 0.7 - - - -
195A ASP* 3.6 15.5 + - - +
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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