Contacts of the helix formed by residues 163 - 179 (chain A) in PDB entry 3EBL
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 PRO 163 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161A ARG 4.3 0.4 - - - +
162A TYR* 1.3 115.0 - - + +
164A CYS* 1.3 67.9 + - - +
165A ALA 3.4 2.2 - - - -
166A TYR* 3.1 12.1 + - + +
167A ASP* 2.9 38.2 + - - +
258A TYR* 3.9 2.7 - - - +
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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
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155A ARG* 3.6 34.9 + - + +
160A HIS* 4.0 27.8 - - + +
161A ARG 3.1 21.0 + - - +
162A TYR* 3.9 0.4 - - - +
163A PRO* 1.3 81.2 - - - +
165A ALA* 1.3 58.9 + - - +
167A ASP* 3.2 9.1 + - - +
168A ASP* 2.9 33.4 + - - -
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Residues in contact with ALA 165 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124A PHE* 4.6 2.0 - - + -
154A TYR* 3.7 35.1 - - + +
155A ARG 3.8 11.3 + - - +
163A PRO 3.4 0.6 - - - -
164A CYS* 1.3 77.3 - - - +
166A TYR* 1.3 63.0 + - - +
168A ASP* 3.3 3.5 + - - +
169A GLY 3.0 17.7 + - - -
203A ILE* 3.8 23.4 - - + +
258A TYR* 3.8 22.8 + - + +
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Residues in contact with TYR 166 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124A PHE* 4.3 0.4 - + - -
162A TYR* 3.5 33.0 - + - -
163A PRO* 3.1 10.4 + - + +
165A ALA* 1.3 74.4 - - - +
167A ASP* 1.3 65.2 + - - +
169A GLY* 3.2 1.7 + - - -
170A TRP* 3.0 24.0 + - - +
202A ASN* 2.6 30.5 + - - -
203A ILE* 3.9 29.4 - - + -
206A HIS* 3.2 41.3 - + + -
207A VAL* 4.0 7.0 - - + +
210A ARG* 5.6 1.1 - - - -
258A TYR* 3.4 27.8 - + - -
269A ALA* 3.3 21.7 + - + +
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Residues in contact with ASP 167 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155A ARG* 4.1 12.2 + - - +
163A PRO* 2.9 38.3 + - - +
164A CYS* 3.4 11.9 - - - +
166A TYR* 1.3 76.0 - - - +
168A ASP* 1.3 59.0 + - - +
170A TRP* 3.2 8.0 + - - +
171A THR* 2.8 33.8 + - - +
210A ARG* 4.1 14.4 + - - +
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Residues in contact with ASP 168 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A VAL* 3.8 12.8 - - - +
76A LEU* 3.5 35.2 - - + +
152A VAL* 4.3 2.8 - - - +
154A TYR* 4.1 9.4 - - + -
155A ARG* 2.9 61.1 + - - +
164A CYS 2.9 18.1 + - - +
165A ALA 3.6 4.9 - - - +
167A ASP* 1.3 73.6 - - - +
169A GLY* 1.3 61.0 + - - +
171A THR* 3.4 2.9 + - - -
172A ALA* 2.9 25.6 + - - +
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Residues in contact with GLY 169 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A ILE* 5.5 0.2 - - - +
119A PHE* 3.4 34.0 - - - -
154A TYR* 5.5 0.2 - - - +
165A ALA 3.0 13.0 + - - -
166A TYR 3.8 2.7 - - - -
168A ASP* 1.3 72.6 - - - +
170A TRP* 1.3 60.9 + - - +
172A ALA* 3.3 2.9 + - - +
173A LEU* 2.9 28.4 + - - +
207A VAL* 3.8 15.1 - - - +
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Residues in contact with TRP 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 TYR 3.0 13.8 + - - +
167A ASP 3.2 7.8 + - - +
169A GLY* 1.3 72.9 - - - +
171A THR* 1.3 68.6 + - - +
173A LEU* 3.1 25.3 + - + +
174A LYS* 3.0 74.7 + - + +
207A VAL* 3.9 9.8 - - + +
210A ARG* 3.2 61.2 - - + +
211A ALA* 3.6 28.3 - - - -
214A GLU* 3.5 27.3 + - + -
216A VAL* 3.9 24.5 - - + -
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Residues in contact with THR 171 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A ILE* 4.1 8.7 - - + +
71A ASP* 3.9 35.6 + - + +
74A VAL* 6.5 0.2 - - - -
76A LEU* 4.0 12.6 - - + -
167A ASP* 2.8 21.3 + - - +
168A ASP* 3.6 7.3 + - - -
170A TRP* 1.3 79.2 - - - +
172A ALA* 1.3 56.8 + - - +
174A LYS* 3.3 12.7 + - - +
175A TRP* 2.9 28.4 + - + +
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Residues in contact with ALA 172 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A ILE* 3.7 21.1 - - + +
78A VAL* 4.7 2.5 - - + -
117A ILE* 4.4 7.2 - - + -
150A VAL* 5.5 1.8 - - + -
152A VAL* 3.6 33.0 - - + -
168A ASP 2.9 17.1 + - - +
169A GLY* 3.6 5.6 - - - +
170A TRP 3.2 0.2 - - - -
171A THR* 1.3 73.5 - - - +
173A LEU* 1.3 66.3 + - - +
175A TRP* 3.8 1.7 - - + +
176A VAL* 3.0 28.1 + - - +
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Residues in contact with LEU 173 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A ILE* 3.7 12.2 - - + +
169A GLY 2.9 17.7 + - - +
170A TRP* 3.6 33.2 - - + +
172A ALA* 1.3 73.7 - - - +
174A LYS* 1.3 65.7 + - + +
176A VAL* 3.2 2.8 + - - +
177A MET* 3.0 55.6 + - + +
192A VAL* 3.8 24.9 - - + -
194A LEU* 4.5 3.6 - - + -
207A VAL* 4.1 14.1 - - + -
211A ALA* 3.9 19.3 - - + -
216A VAL* 4.0 8.5 - - + -
218A VAL* 4.4 6.3 - - + -
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Residues in contact with LYS 174 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170A TRP* 3.0 70.7 + - + +
171A THR* 3.8 10.6 + - - +
173A LEU* 1.3 77.2 - - + +
175A TRP* 1.3 63.1 + - - +
177A MET* 3.4 9.1 + - - +
178A SER* 3.3 23.6 + - - -
216A VAL* 5.9 3.6 - - + -
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Residues in contact with TRP 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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68A HIS* 3.5 27.9 + + - -
70A ILE* 3.6 47.0 - - + +
78A VAL* 4.5 0.7 - - + -
80A ILE* 3.7 26.9 - - + -
104A LEU* 5.4 7.0 - - + -
150A VAL* 4.5 9.9 - - + -
171A THR* 2.9 18.5 + - + +
172A ALA* 3.8 3.8 - - - +
174A LYS* 1.3 76.8 - - - +
176A VAL* 1.3 94.5 + - + +
178A SER* 3.0 9.2 + - - -
179A GLN* 3.0 62.8 + - + +
182A MET* 4.1 16.8 - - + -
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Residues in contact with VAL 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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115A VAL* 3.8 24.2 - - + -
117A ILE* 3.8 20.4 - - + -
150A VAL* 4.1 18.4 - - + -
172A ALA 3.0 20.9 + - - +
173A LEU 3.7 3.8 - - - +
175A TRP* 1.3 97.0 - - + +
177A MET* 1.3 62.9 - - - +
178A SER 3.1 0.9 + - - -
179A GLN 3.2 10.0 + - - +
182A MET* 3.4 28.2 - - + +
190A ALA* 4.3 1.3 - - + +
192A VAL* 4.0 19.5 - - + -
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Residues in contact with MET 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 LEU* 3.0 39.0 + - + +
174A LYS* 3.8 7.4 - - - +
175A TRP 3.3 0.4 - - - -
176A VAL* 1.3 76.1 - - - +
178A SER* 1.3 51.9 + - - +
179A GLN 4.4 0.3 - - - +
183A ARG* 2.8 38.7 + - - +
189A GLN* 6.5 0.2 - - - -
190A ALA* 3.9 19.9 - - - +
192A VAL* 3.7 21.5 - - + -
216A VAL* 3.1 34.1 - - + -
217A LYS* 3.2 23.3 - - + +
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Residues in contact with SER 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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174A LYS 3.3 12.9 + - - -
175A TRP* 3.0 16.9 + - - -
176A VAL 3.1 0.8 - - - -
177A MET* 1.3 77.2 - - - +
179A GLN* 1.3 71.3 + - - +
180A PRO* 3.5 8.8 - - - +
183A ARG* 4.1 10.3 + - - +
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Residues in contact with GLN 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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104A LEU* 4.1 25.2 - - + +
175A TRP* 3.0 71.5 + - + +
176A VAL 3.2 4.0 + - - +
178A SER* 1.3 92.8 + - - +
180A PRO* 1.4 72.1 - - + +
181A PHE* 5.0 1.6 - - + -
182A MET* 3.2 33.2 + - + +
183A ARG* 3.7 12.8 - - - +
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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