Contacts of the helix formed by residues 154 - 171 (chain A) in PDB entry 1RPK
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 ASN 154 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122A HIS* 3.7 37.8 + - - -
123A MET* 4.3 8.6 - - + +
137A ASN* 4.6 2.7 - - - +
151A ASP* 3.0 28.6 + - + +
153A LEU* 1.3 79.2 - - - +
155A ASP* 1.3 64.3 + - - +
156A ARG* 2.9 33.6 + - - +
157A VAL* 3.0 21.3 + - + +
158A GLN* 3.1 24.2 + - - +
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Residues in contact with ASP 155 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153A LEU 3.5 7.8 + - - +
154A ASN* 1.3 74.1 + - - +
156A ARG* 1.3 63.9 + - - +
158A GLN* 3.4 9.7 + - - +
159A ARG* 3.1 35.1 + - - +
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Residues in contact with ARG 156 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115A GLY* 2.9 30.9 + - - -
118A ASP* 3.7 18.4 + - - +
119A TRP* 4.1 5.1 - - - +
123A MET* 3.4 30.0 - - + +
154A ASN* 2.9 13.1 + - - +
155A ASP* 1.3 77.3 - - - +
157A VAL* 1.3 58.6 + - - +
159A ARG* 3.5 27.7 - - - +
160A GLU* 2.7 61.5 + - - +
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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
----------------------------------------------------------
119A TRP* 3.9 16.6 - - + -
123A MET* 3.6 35.4 - - + -
150A ILE* 3.5 26.0 - - + -
151A ASP 3.7 11.0 - - - +
152A HIS* 3.9 2.5 - - - +
154A ASN* 3.0 28.0 + - + +
156A ARG* 1.3 75.9 - - - +
158A GLN* 1.3 64.0 + - - +
160A GLU 3.9 0.2 - - - -
161A LEU* 2.9 36.6 + - + +
193A TYR* 3.8 14.4 - - - +
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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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152A HIS 2.9 29.2 + - - +
153A LEU* 4.2 9.4 + - - +
154A ASN 3.1 10.3 + - - +
155A ASP* 3.8 9.9 - - - +
157A VAL* 1.3 79.4 - - - +
159A ARG* 1.3 63.4 + - - +
162A LYS* 3.0 38.3 + - - +
189A MET* 3.8 18.0 - - - +
192A VAL* 3.8 33.8 - - + +
193A TYR* 3.6 16.4 - - + +
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Residues in contact with ARG 159 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155A ASP* 3.1 23.8 + - - +
156A ARG* 3.5 44.4 - - - +
158A GLN* 1.3 79.8 - - - +
160A GLU* 1.3 65.9 + - + +
162A LYS* 3.5 9.8 + - - +
163A GLU* 3.1 27.9 + - + +
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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
----------------------------------------------------------
58A TYR* 4.3 1.9 + - - -
115A GLY 4.8 0.2 - - - -
116A ARG* 4.0 10.3 - - + +
117A LEU* 2.7 45.8 + - + +
119A TRP* 2.8 22.6 + - - +
156A ARG* 2.7 56.0 + - + +
157A VAL 4.2 0.9 - - - +
159A ARG* 1.3 82.7 + - + +
161A LEU* 1.3 58.7 + - - +
163A GLU* 3.3 17.4 + - - +
164A TRP* 2.9 28.1 + - - +
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Residues in contact with LEU 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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57A LEU* 3.9 28.0 - - + -
91A ILE* 4.1 16.4 - - + +
117A LEU* 4.0 7.0 - - + -
119A TRP* 3.9 20.0 - - + -
150A ILE* 5.1 0.7 - - + -
152A HIS* 3.6 31.6 - - + -
157A VAL* 2.9 24.8 + - + +
160A GLU* 1.3 72.4 - - - +
162A LYS* 1.3 62.2 + - - +
164A TRP* 3.1 12.1 + - + +
165A LEU* 2.8 38.9 + - + +
193A TYR* 3.6 23.6 - - + +
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Residues in contact with LYS 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 30.7 + - - +
159A ARG* 3.7 8.1 - - - +
161A LEU* 1.3 79.2 - - - +
163A GLU* 1.3 55.9 + - - +
165A LEU* 3.3 8.1 + - - +
166A LEU* 3.0 36.9 + - + +
192A VAL* 3.9 28.4 + - + +
193A TYR* 3.7 20.4 - - + -
196A GLY* 3.9 28.8 - - - +
197A THR* 4.0 7.5 - - + +
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Residues in contact with GLU 163 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A TYR* 3.7 7.9 + - - +
116A ARG* 3.1 43.9 + - - +
159A ARG* 3.1 19.2 + - + +
160A GLU* 3.5 12.8 - - - +
161A LEU 3.2 0.2 - - - -
162A LYS* 1.3 77.9 - - - +
164A TRP* 1.3 61.4 + - - +
166A LEU* 3.5 9.1 + - - +
167A TRP* 3.1 21.9 + - + +
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Residues in contact with TRP 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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43A PRO* 5.4 4.3 - - + -
44A SER* 3.6 20.0 - - - -
57A LEU* 3.1 53.0 + - + -
58A TYR* 3.2 43.2 + + + +
88A ASP 5.7 0.9 - - - -
89A ILE* 4.2 12.1 - - + -
90A VAL 5.2 3.8 - - - -
91A ILE* 3.9 24.9 - - + -
117A LEU* 4.5 4.3 - - + -
160A GLU 2.9 17.4 + - - +
161A LEU* 3.1 11.9 + - + +
163A GLU* 1.3 76.8 - - - +
165A LEU* 1.3 84.6 + - + +
167A TRP* 3.1 9.0 + + - +
168A LEU* 2.9 56.7 + - + +
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Residues in contact with LEU 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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89A ILE* 3.6 43.3 - - + -
91A ILE* 5.5 2.7 - - + -
161A LEU* 2.8 25.3 + - + +
162A LYS 3.6 4.0 - - - +
164A TRP* 1.3 89.2 - - + +
166A LEU* 1.3 61.2 + - - +
168A LEU* 3.1 13.0 + - + -
169A LYS* 3.3 2.6 + - - +
177A TRP* 3.1 37.8 - - + +
179A LEU* 6.6 0.4 - - + -
193A TYR* 4.0 33.7 - - + +
197A THR* 3.6 24.2 - - + +
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Residues in contact with LEU 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 LYS* 3.0 24.1 + - + +
163A GLU* 3.8 8.3 - - - +
164A TRP 3.3 0.2 - - - -
165A LEU* 1.3 75.0 - - - +
167A TRP* 1.3 51.1 + - - +
169A LYS* 3.2 16.8 + - - +
170A SER* 2.8 35.9 + - - -
196A GLY 4.3 8.3 - - - +
197A THR* 3.9 36.6 - - + +
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Residues in contact with TRP 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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58A TYR* 3.6 59.1 - + + +
60A ILE* 3.7 25.1 - - + -
68A ALA* 6.2 1.3 - - + -
163A GLU* 3.1 13.8 + - + +
164A TRP* 3.1 16.0 + + - +
166A LEU* 1.3 73.2 - - - +
168A LEU* 1.3 79.4 + - + +
169A LYS 3.1 1.8 - - - -
170A SER* 3.5 10.8 - - - -
171A ASP* 2.7 74.3 + - + +
172A LEU* 4.5 6.1 - - + -
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Residues in contact with LEU 168 (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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43A PRO* 4.7 7.4 - - + -
60A ILE* 4.5 6.3 - - + -
87A ALA* 4.8 4.5 - - + -
89A ILE* 3.6 31.9 - - + -
164A TRP* 2.9 45.8 + - + +
165A LEU* 3.1 13.0 + - + +
167A TRP* 1.3 91.8 - - + +
169A LYS* 1.3 57.6 + - - +
172A LEU* 3.2 32.9 - - + +
173A GLY 3.2 9.7 + - - -
174A PHE* 3.1 23.1 + - + +
177A TRP* 4.0 14.6 - - + -
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Residues in contact with LYS 169 (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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165A LEU 3.5 4.7 - - - +
166A LEU* 3.2 18.3 + - - +
167A TRP 3.1 0.2 - - - -
168A LEU* 1.3 77.7 - - - +
170A SER* 1.3 58.7 + - - +
173A GLY* 2.9 28.1 + - - -
174A PHE 3.3 25.3 - - - +
175A ASP* 4.4 12.3 + - - +
177A TRP* 3.4 29.2 - - + -
197A THR 2.8 27.6 + - - +
198A SER* 3.0 20.6 + - - +
199A PRO* 4.6 1.3 - - + +
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Residues in contact with SER 170 (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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166A LEU 2.8 22.1 + - - -
167A TRP* 3.5 13.0 - - - -
169A LYS* 1.3 76.7 - - - +
171A ASP* 1.3 61.0 + - - +
173A GLY* 4.5 1.1 + - - -
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Residues in contact with ASP 171 (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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68A ALA* 5.5 1.0 - - - +
72A LYS* 2.9 41.1 + - - +
167A TRP* 2.7 58.3 + - + +
170A SER* 1.3 77.1 + - - +
172A LEU* 1.3 68.0 + - + +
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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
------------------------------------------------------------
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