Contacts of the helix formed by residues 162 - 180 (chain A) in PDB entry 3A3K
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 ARG 162 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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88A TYR* 3.4 27.3 + - - -
156A ASP* 3.4 22.4 + - + +
157A ARG 5.9 0.7 - - - +
159A GLY* 5.3 2.9 - - - -
160A ASP* 3.0 23.0 + - - +
161A ASP* 1.3 77.7 - - - +
163A PRO* 1.3 72.7 - - - +
164A CYS 3.2 3.2 + - - -
165A PHE* 3.2 64.2 + - + +
166A PHE* 3.3 13.0 + - + -
187A GLU* 4.9 12.7 + - - -
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Residues in contact with PRO 163 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130A HIS* 4.4 3.1 + - - +
156A ASP* 3.3 13.9 - - - +
157A ARG 6.0 0.2 - - - +
160A ASP* 4.0 9.0 - - - +
161A ASP* 3.1 12.5 - - + +
162A ARG* 1.3 88.3 - - - +
164A CYS* 1.3 57.8 + - + +
166A PHE* 3.3 5.7 + - + +
167A ILE* 2.9 41.4 + - + +
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Residues in contact with CYS 164 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154A TYR* 4.2 3.4 - - + -
155A ALA 3.2 27.6 - - - +
156A ASP* 2.9 12.0 + - - +
163A PRO* 1.3 74.5 - - - +
165A PHE* 1.3 66.4 + - - +
167A ILE* 3.6 1.9 - - - +
168A VAL* 3.0 30.7 + - - +
213A CYS* 2.1 64.4 - - + +
214A SER* 3.7 4.5 - - - -
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Residues in contact with PHE 165 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154A TYR* 3.9 35.3 - + + -
156A ASP* 2.9 17.2 + - - +
162A ARG* 3.2 56.5 + - + +
164A CYS* 1.3 74.1 - - - +
166A PHE* 1.3 87.0 + + - +
168A VAL* 3.3 1.4 + - - +
169A GLU* 2.8 55.0 + - + +
187A GLU* 5.8 0.9 - - - +
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Residues in contact with PHE 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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87A VAL* 3.6 34.1 - - + -
88A TYR* 3.7 33.4 - + - -
111A ALA* 3.7 20.0 - - + -
112A LEU 5.2 2.1 + - - -
130A HIS* 3.3 24.3 - - + +
161A ASP 3.2 28.7 - - - -
162A ARG* 3.3 15.2 + - + -
163A PRO* 3.7 6.1 - - + +
165A PHE* 1.3 88.8 - + - +
167A ILE* 1.3 65.8 + - - +
169A GLU* 3.4 25.3 - - - +
170A GLY* 3.1 17.2 + - - -
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Residues in contact with ILE 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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130A HIS* 3.4 31.4 - - + +
133A LEU* 3.6 27.1 - - + +
163A PRO* 2.9 30.6 + - + +
164A CYS* 3.6 6.7 - - - +
165A PHE 3.3 0.2 - - - -
166A PHE* 1.3 74.3 - - - +
168A VAL* 1.3 59.5 + - + +
170A GLY* 3.3 2.8 + - - -
171A LEU* 2.8 27.4 + - + +
213A CYS* 3.7 26.7 - - - -
241A LEU* 4.4 15.7 - - + +
243A VAL* 4.3 26.0 - - + -
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Residues in contact with VAL 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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152A VAL* 3.6 34.1 - - + -
154A TYR* 3.6 42.2 - - + -
164A CYS 3.0 17.9 + - - +
165A PHE 3.8 2.2 - - - +
167A ILE* 1.3 75.3 - - + +
169A GLU* 1.3 58.3 + - - +
171A LEU* 3.1 6.0 + - + -
172A TYR* 2.7 45.8 + - + +
185A HIS* 4.7 9.9 - - + -
213A CYS* 4.4 8.3 - - + -
241A LEU* 5.1 2.2 - - + -
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Residues in contact with GLU 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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112A LEU* 4.0 32.7 + - + +
113A GLY 5.0 1.7 + - - -
165A PHE* 2.8 48.0 + - + +
166A PHE* 3.4 28.4 - - - +
168A VAL* 1.3 72.0 - - - +
170A GLY* 1.3 63.4 + - - +
172A TYR* 4.0 4.5 - - - +
173A MET* 3.2 34.4 + - + +
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Residues in contact with GLY 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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112A LEU* 4.5 15.2 - - - +
130A HIS* 3.9 22.7 - - - -
131A VAL* 4.1 8.3 - - - +
166A PHE 3.1 15.3 + - - -
167A ILE 3.6 3.4 - - - -
169A GLU* 1.3 76.1 - - - +
171A LEU* 1.3 63.7 + - - +
173A MET* 3.6 0.7 + - - +
174A ARG* 3.3 24.8 + - - +
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Residues in contact with LEU 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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130A HIS 4.0 1.8 + - - -
133A LEU* 4.1 14.8 - - + -
134A GLY* 4.2 11.9 - - - +
137A VAL* 4.0 29.2 - - + -
152A VAL* 4.6 19.7 - - + -
167A ILE* 2.8 20.2 + - + +
168A VAL* 3.1 5.6 + - + +
170A GLY* 1.3 72.0 - - - +
172A TYR* 1.3 62.6 + - - +
174A ARG* 3.9 0.7 - - - +
175A VAL* 2.9 51.3 + - + +
183A VAL* 5.1 4.0 - - + -
211A TYR* 4.7 10.8 - - + -
241A LEU* 3.7 31.0 - - + -
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Residues in contact with TYR 172 (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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168A VAL* 2.7 29.1 + - + +
169A GLU* 4.0 4.3 - - - +
171A LEU* 1.3 80.0 - - + +
173A MET* 1.3 89.3 + - + +
175A VAL* 3.9 1.9 - - - +
176A ARG* 3.0 66.8 + - + +
183A VAL* 3.5 44.2 - - + -
185A HIS* 4.0 23.2 + + - -
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Residues in contact with MET 173 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112A LEU* 3.8 34.1 - - + -
131A VAL* 5.7 0.2 - - + -
169A GLU* 3.2 22.5 + - + +
170A GLY 4.2 2.2 - - - +
172A TYR* 1.3 98.2 - - + +
174A ARG* 1.3 62.7 + - - +
176A ARG* 3.9 3.6 - - - +
177A GLU* 3.1 24.7 + - - +
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Residues in contact with ARG 174 (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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131A VAL* 3.4 53.5 - - + +
132A LYS* 5.4 3.2 - - - +
134A GLY* 3.7 16.4 - - - -
135A ASP* 3.2 36.7 + - - +
170A GLY 3.3 16.2 + - - +
173A MET* 1.3 78.6 - - - +
175A VAL* 1.3 63.2 + - - +
177A GLU* 3.3 23.9 + - - +
178A ARG* 3.2 34.2 + - - +
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Residues in contact with VAL 175 (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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134A GLY* 3.6 21.5 - - - +
137A VAL* 3.7 26.9 - - + -
138A THR* 4.1 7.0 - - - +
171A LEU* 2.9 31.2 + - + +
172A TYR* 4.1 2.2 - - - +
174A ARG* 1.3 76.5 - - - +
176A ARG* 1.3 57.4 + - - +
179A LEU* 3.0 40.7 + - + +
180A ASN 3.9 0.2 + - - -
181A ILE* 3.7 31.5 - - + +
183A VAL* 4.3 7.2 - - + -
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Residues in contact with ARG 176 (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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172A TYR* 3.0 63.0 + - + +
173A MET* 3.9 5.4 - - - +
175A VAL* 1.3 75.5 - - - +
177A GLU* 1.3 62.6 + - - +
180A ASN* 3.3 40.1 + - - +
181A ILE 3.3 22.3 + - - +
182A THR* 5.4 2.3 - - - +
183A VAL* 4.2 15.9 - - + +
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Residues in contact with GLU 177 (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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173A MET 3.1 18.1 + - - +
174A ARG* 3.5 30.3 + - - +
175A VAL 3.2 0.2 - - - -
176A ARG* 1.3 78.9 - - - +
178A ARG* 1.3 63.8 + - + +
180A ASN* 5.0 4.9 + - - +
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Residues in contact with ARG 178 (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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135A ASP* 2.8 45.7 + - - +
138A THR* 3.8 30.1 - - + +
142A ARG* 3.2 26.7 + - - +
174A ARG* 3.2 36.9 + - - +
177A GLU* 1.3 85.7 - - - +
179A LEU* 1.3 61.0 + - - +
180A ASN* 3.8 3.2 + - - -
399A GLN* 2.7 34.7 + - - +
504A SO4 2.7 49.0 + - - +
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Residues in contact with LEU 179 (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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138A THR* 3.8 24.9 - - + +
141A HIS* 3.5 35.9 - - + +
142A ARG* 3.4 39.0 - - + +
146A TRP 4.8 2.0 - - - +
147A GLU* 4.7 7.6 - - + +
175A VAL* 3.0 27.1 + - + +
178A ARG* 1.3 79.7 - - - +
180A ASN* 1.3 66.8 + - - +
181A ILE* 2.9 29.2 + - + +
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Residues in contact with ASN 180 (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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147A GLU 5.6 0.4 - - - -
175A VAL 3.9 0.4 + - - -
176A ARG* 3.3 31.8 + - - +
177A GLU 5.0 4.8 + - - +
178A ARG 5.4 2.4 + - - -
179A LEU* 1.3 78.3 - - - +
181A ILE* 1.3 64.1 + - - +
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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
------------------------------------------------------------
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