Contacts of the helix formed by residues 161 - 178 (chain A) in PDB entry 3ROT
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 HIS 161 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30A HIS* 3.6 20.2 + + - -
89A PRO* 3.9 13.2 - - + +
113A THR* 3.2 27.3 + - + +
131A ASN* 5.3 0.7 - - - -
158A GLN* 3.0 38.0 + - + +
159A PRO 3.3 1.0 + - - -
160A GLY* 1.3 72.9 - - - +
162A ILE* 1.3 62.1 + - - +
163A GLY* 2.8 34.8 + - - -
164A LEU* 3.0 30.8 + - + +
165A GLU* 3.1 23.0 + - - +
167A ARG* 6.0 0.2 - - - -
317A GOL 2.8 25.8 + - - -
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Residues in contact with ILE 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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88A ILE 3.3 22.4 - - - +
89A PRO 3.3 22.2 + - - +
90A SER* 3.7 9.6 - - - +
91A ASP* 3.7 26.7 - - - +
113A THR* 3.6 8.3 - - + -
114A ARG 3.3 18.6 - - - +
115A PRO* 3.8 12.3 - - + -
116A LYS 4.9 0.2 - - - +
160A GLY 3.1 7.1 + - - +
161A HIS* 1.3 71.8 + - - +
163A GLY* 1.3 63.8 - - - +
165A GLU* 3.5 21.1 + - - +
166A LYS* 3.3 27.7 + - - +
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Residues in contact with GLY 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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113A THR* 3.8 7.0 - - - -
131A ASN* 3.3 30.7 - - - -
161A HIS* 2.8 18.7 + - - -
162A ILE* 1.3 79.9 - - - +
164A LEU* 1.3 65.9 + - - +
166A LYS* 3.2 15.3 + - - +
167A ARG* 3.2 9.9 + - - +
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Residues in contact with LEU 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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156A ASN* 3.9 25.8 - - - +
157A PRO* 4.2 7.9 - - + -
158A GLN* 4.0 23.8 - - + +
161A HIS* 3.0 31.4 + - + +
163A GLY* 1.3 74.7 - - - +
165A GLU* 1.3 65.6 + - - +
167A ARG* 3.2 42.0 + - - +
168A ALA* 3.0 24.1 + - - +
214A LEU* 3.9 11.7 - - + +
215A THR* 3.6 25.8 - - + -
317A GOL 4.8 1.8 - - - +
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Residues in contact with GLU 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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156A ASN* 5.0 8.9 - - - +
159A PRO* 6.0 0.2 - - + -
160A GLY* 3.9 20.5 + - - +
161A HIS 3.1 20.1 + - - +
162A ILE* 3.7 23.6 - - - +
163A GLY 3.2 0.4 - - - -
164A LEU* 1.3 76.6 - - - +
166A LYS* 1.3 59.9 + - + +
168A ALA* 3.4 6.3 + - - +
169A TYR* 2.9 30.0 + - - +
184A GLU* 6.0 0.2 - - - -
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Residues in contact with LYS 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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116A LYS* 5.9 11.6 - - - +
131A ASN* 3.6 18.4 - - + -
132A LEU* 3.6 36.6 - - + +
162A ILE* 3.3 14.8 + - - +
163A GLY* 3.2 9.9 + - - +
165A GLU* 1.3 79.0 - - + +
167A ARG* 1.3 56.1 + - - +
169A TYR* 3.6 7.4 - - + +
170A GLY 2.9 23.9 + - - -
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Residues in contact with ARG 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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112A ASP 5.5 0.6 + - - -
131A ASN* 2.8 43.3 + - - +
135A GLY* 3.5 3.9 - - - -
161A HIS* 6.0 0.4 - - - -
163A GLY 3.2 7.7 + - - +
164A LEU* 3.2 27.5 + - - +
166A LYS* 1.3 77.6 - - - +
168A ALA* 1.3 63.2 + - - +
170A GLY 3.2 1.7 + - - -
171A ILE* 2.9 28.6 + - - +
214A LEU* 2.7 43.0 + - + -
243A PHE* 3.6 42.8 - - + +
264A GLN* 2.9 25.5 + - - +
317A GOL 2.7 41.0 + - - -
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Residues in contact with ALA 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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154A VAL* 4.4 5.4 - - + -
156A ASN* 5.1 0.2 - - - +
164A LEU 3.0 15.1 + - - +
165A GLU* 3.7 6.5 - - - +
167A ARG* 1.3 75.9 - - - +
169A TYR* 1.3 63.8 + - - +
171A ILE* 3.1 6.3 + - - +
172A LYS* 2.9 34.9 + - - +
184A GLU* 3.2 32.1 - - - +
214A LEU* 4.1 16.7 - - + +
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Residues in contact with TYR 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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132A LEU* 3.6 22.2 - - + -
136A LYS* 5.0 2.0 - - - -
165A GLU 2.9 17.7 + - - +
166A LYS* 3.6 9.9 - - + +
168A ALA* 1.3 76.3 - - - +
170A GLY* 1.3 62.9 + - - +
172A LYS* 3.3 14.1 + - + +
173A THR* 3.1 50.9 + - + +
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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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132A LEU* 3.7 31.4 - - - +
136A LYS* 3.4 24.2 - - - -
166A LYS 2.9 12.5 + - - -
167A ARG 3.6 2.9 - - - -
169A TYR* 1.3 75.8 - - - +
171A ILE* 1.3 60.5 + - - +
173A THR* 2.7 20.0 + - - -
174A ILE* 3.6 2.3 - - - +
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Residues in contact with ILE 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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135A GLY 3.3 21.3 - - - +
138A LEU* 4.4 1.8 - - + -
139A GLY* 4.4 5.5 - - - +
154A VAL* 4.3 9.4 - - + -
167A ARG 2.9 17.5 + - - +
168A ALA* 3.1 8.0 + - - +
170A GLY* 1.3 77.3 - - - +
172A LYS* 1.3 61.6 + - - +
174A ILE* 3.2 7.1 + - - +
175A LEU* 3.1 39.3 + - + +
212A PHE* 3.7 51.1 - - + -
214A LEU* 4.1 19.7 - - + -
243A PHE* 4.2 15.9 - - + -
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Residues in contact with LYS 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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154A VAL* 5.0 10.3 - - + -
168A ALA* 2.9 26.8 + - - +
169A TYR* 3.7 12.3 - - + +
171A ILE* 1.3 74.4 - - + +
173A THR* 1.3 55.9 + - + +
175A LEU* 3.6 8.5 - - + +
176A GLN* 2.7 38.6 + - - +
182A PHE* 3.6 38.7 - - + -
184A GLU* 2.5 49.4 + - - +
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Residues in contact with THR 173 (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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136A LYS* 3.0 26.0 + - - +
169A TYR* 3.1 46.1 + - + +
170A GLY 2.7 21.1 + - - -
172A LYS* 1.3 76.3 - - + +
174A ILE* 1.3 65.8 + - - +
176A GLN* 3.7 9.2 - - - +
177A ASP* 3.0 32.7 + - - +
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Residues in contact with ILE 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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136A LYS* 3.3 34.3 - - + +
139A GLY* 3.7 19.3 - - - -
140A GLU* 3.7 25.6 - - + +
143A LEU* 3.6 23.8 - - + -
170A GLY 3.6 12.1 - - - +
171A ILE 3.2 6.6 + - - +
173A THR* 1.3 84.0 + - - +
175A LEU* 1.3 63.6 + - + +
177A ASP* 3.2 16.8 + - + +
178A LYS* 3.3 22.0 + - + +
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Residues in contact with LEU 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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139A GLY* 5.2 1.6 - - - +
143A LEU* 4.0 28.5 - - + -
152A ALA* 3.7 16.8 - - + -
154A VAL* 5.0 3.4 - - + -
171A ILE* 3.1 35.9 + - + +
172A LYS* 3.7 6.3 - - - +
174A ILE* 1.3 78.7 - - + +
176A GLN* 1.3 60.9 + - - +
178A LYS 3.4 1.2 + - - -
179A GLY 3.2 3.5 + - - -
180A ILE* 2.9 47.0 + - + +
182A PHE* 3.7 36.1 - - + -
210A ILE* 5.8 1.1 - - + -
212A PHE* 4.1 16.6 - - + -
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Residues in contact with GLN 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 LYS 2.7 21.8 + - - +
173A THR* 3.7 9.4 - - - +
175A LEU* 1.3 72.3 - - - +
177A ASP* 1.3 67.6 + - - +
179A GLY* 3.0 14.9 + - - -
180A ILE 4.9 0.9 - - - -
182A PHE* 4.1 18.7 - - + -
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Residues in contact with ASP 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 THR* 3.0 24.1 + - - +
174A ILE* 3.2 15.0 + - + +
176A GLN* 1.3 81.4 + - - +
178A LYS* 1.3 77.1 + - + +
179A GLY 3.7 0.2 + - - -
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Residues in contact with LYS 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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143A LEU* 3.2 34.3 - - + -
174A ILE* 3.3 14.0 + - - +
175A LEU 3.4 0.2 + - - -
176A GLN 3.1 0.6 - - - -
177A ASP* 1.3 93.8 + - - +
179A GLY* 1.3 63.7 + - - +
180A ILE* 3.4 18.2 + - + +
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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