Contacts of the helix formed by residues 163 - 179 (chain B) in PDB entry 3L49
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 VAL 163 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1B UNL 4.4 10.5 - - - -
71B ARG* 6.0 1.6 - - - +
95B LEU* 4.1 17.9 - - + -
96B GLY* 3.5 24.7 - - - +
97B ASN* 5.2 1.6 - - - +
160B PHE* 3.0 42.6 + - + +
161B TYR 3.7 2.5 - - - +
162B SER* 1.3 78.3 - - - +
164B PRO* 1.3 61.7 - - + +
165B VAL* 3.9 24.2 - - + +
166B CYS* 3.0 24.2 + - + +
167B LYS 3.1 9.7 + - - -
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Residues in contact with PRO 164 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96B GLY 4.1 7.9 - - - +
98B LEU* 3.8 33.2 - - + -
119B ASP 4.1 4.3 - - - +
120B THR* 4.4 7.9 - - + +
121B ALA* 4.0 34.1 - - + +
162B SER 3.5 8.5 - - - +
163B VAL* 1.3 87.8 - - + +
165B VAL* 1.3 61.9 + - + +
167B LYS* 3.2 16.1 + - + +
168B ILE* 3.1 28.8 + - + +
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Residues in contact with VAL 165 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1B UNL 4.3 2.0 - - + +
95B LEU* 4.3 7.0 - - + -
119B ASP* 3.3 44.6 - - + +
121B ALA* 6.3 0.4 - - + -
130B THR* 4.0 2.7 - - - +
133B ASN* 3.4 30.4 - - - +
163B VAL* 3.3 15.7 - - + +
164B PRO* 1.3 78.0 - - + +
166B CYS* 1.3 60.4 + - - +
168B ILE* 3.7 8.8 + - + +
169B ARG* 3.2 56.5 + - - +
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Residues in contact with CYS 166 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1B UNL 4.3 17.7 - - - -
158B ASN* 5.0 1.9 - - - +
160B PHE* 3.2 33.7 - - - +
161B TYR* 4.6 2.1 - - - -
163B VAL* 3.0 6.5 + - + +
165B VAL* 1.3 79.4 - - - +
167B LYS* 1.3 60.1 + - - +
169B ARG* 3.4 8.8 + - - +
170B TYR* 3.0 29.1 + - - +
224B CYS* 2.0 56.8 - - - +
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Residues in contact with LYS 167 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175A TYR* 3.5 15.5 + - + +
178A GLU* 5.1 4.2 + - - -
161B TYR* 3.3 54.6 + - + +
163B VAL 3.1 6.4 + - - +
164B PRO* 3.2 23.3 + - + +
166B CYS* 1.3 75.2 - - - +
168B ILE* 1.3 60.2 + - + +
170B TYR* 3.4 0.9 + - - +
171B ASP* 2.9 62.4 + - - +
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Residues in contact with ILE 168 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175A TYR* 3.4 15.7 - - + +
179A ALA* 6.3 0.2 - - + -
121B ALA* 5.6 8.7 - - + -
133B ASN* 3.5 40.4 - - + +
134B TYR* 3.6 48.9 - - + +
164B PRO* 3.1 20.8 + - + +
165B VAL* 3.8 8.3 - - + +
166B CYS 3.4 0.2 - - - -
167B LYS* 1.3 78.2 - - + +
169B ARG* 1.3 57.7 + - - +
171B ASP* 4.1 0.3 - - - +
172B GLN* 3.0 32.1 + - + +
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Residues in contact with ARG 169 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1B UNL 2.9 27.5 + - - -
119B ASP* 4.5 0.6 + - - -
133B ASN* 2.8 41.9 + - + +
136B ILE* 4.5 5.8 - - + +
137B GLY* 4.2 13.2 - - - -
165B VAL* 3.2 36.5 + - - +
166B CYS* 3.8 9.8 - - - +
167B LYS 3.3 0.2 - - - -
168B ILE* 1.3 77.3 - - - +
170B TYR* 1.3 63.1 + - - +
172B GLN* 4.0 2.1 - - - +
173B MET* 3.2 16.8 + - - +
222B TRP* 3.3 17.3 - - + -
224B CYS* 2.8 46.3 + - + -
249B VAL* 3.6 24.5 - - + +
272B GLN* 3.1 25.9 + - - +
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Residues in contact with TYR 170 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156B VAL* 3.9 3.1 - - + -
158B ASN* 3.7 25.6 - - + +
161B TYR* 3.4 29.4 - + + -
166B CYS 3.0 17.8 + - - +
167B LYS 3.8 2.0 - - - +
169B ARG* 1.3 74.9 - - - +
171B ASP* 1.3 64.0 + - - +
173B MET* 3.1 27.7 + - + +
174B LYS* 2.9 62.4 + - + +
189B GLU* 2.6 43.7 + - - -
222B TRP* 3.6 18.1 - + + -
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Residues in contact with ASP 171 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175A TYR* 2.6 41.1 + - + +
161B TYR* 2.6 23.7 + - - -
167B LYS* 2.9 40.3 + - - +
170B TYR* 1.3 78.2 - - - +
172B GLN* 1.3 54.8 + - - +
174B LYS* 3.3 10.2 + - - +
175B TYR* 2.8 36.8 + - - +
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Residues in contact with GLN 172 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134A TYR* 4.8 1.9 - - - +
172A GLN* 2.9 42.8 + - - +
175A TYR* 3.6 25.8 - - + -
133B ASN 4.3 0.7 - - - +
134B TYR* 3.3 36.0 - - - +
137B GLY* 3.7 5.8 - - - -
138B ALA* 3.7 23.3 - - - +
168B ILE* 3.0 24.9 + - + +
171B ASP* 1.3 74.6 + - - +
173B MET* 1.3 60.4 + - - +
175B TYR* 3.8 7.0 - - - +
176B VAL* 3.0 36.2 + - - +
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Residues in contact with MET 173 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137B GLY 4.3 1.9 + - - +
141B ALA* 3.7 22.9 - - + -
144B MET* 4.1 13.0 - - + -
156B VAL* 4.1 22.4 - - + -
169B ARG 3.2 13.1 + - - +
170B TYR* 3.1 45.2 + - + +
172B GLN* 1.3 75.9 - - - +
174B LYS* 1.3 65.9 + - - +
176B VAL* 3.5 1.6 + - - +
177B LEU* 3.1 50.9 + - + +
185B ILE* 4.1 11.2 - - + -
222B TRP* 3.9 28.3 - - + +
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Residues in contact with LYS 174 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170B TYR* 2.9 53.1 + - + +
171B ASP* 3.8 10.7 + - - +
173B MET* 1.3 83.0 - - + +
175B TYR* 1.3 63.9 + - - +
177B LEU* 3.3 12.8 + - + +
178B GLU* 3.3 23.7 + - - +
185B ILE* 4.2 17.5 - - + -
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Residues in contact with TYR 175 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134A TYR* 3.5 36.7 + + - -
167A LYS* 3.7 10.4 - - + +
168A ILE* 3.5 22.5 - - + +
171A ASP* 2.5 44.4 + - + +
172A GLN* 4.0 16.6 - - - -
171B ASP 2.8 19.0 + - - +
172B GLN* 3.8 9.0 - - - +
174B LYS* 1.3 74.4 - - - +
176B VAL* 1.3 65.2 - - - +
178B GLU* 3.3 45.8 - - + +
179B ALA* 4.1 1.6 + - - +
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Residues in contact with VAL 176 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134A TYR* 3.9 31.1 + - + +
138B ALA* 4.0 24.2 - - - +
141B ALA* 4.0 17.9 - - + +
142B LEU* 3.8 32.8 - - + +
145B VAL* 4.5 2.7 - - + -
172B GLN* 3.0 22.7 + - - +
173B MET 3.8 4.5 - - - +
175B TYR* 1.3 74.5 - - - +
177B LEU* 1.3 64.0 + - + +
179B ALA* 3.3 14.2 + - - +
180B PHE* 3.4 20.3 - - + -
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Residues in contact with LEU 177 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141B ALA* 4.4 11.0 - - + +
144B MET* 4.1 21.5 - - + -
145B VAL* 5.3 5.2 - - + -
154B VAL* 4.6 8.7 - - + -
173B MET* 3.1 33.4 + - + +
174B LYS* 3.7 7.0 - - - +
175B TYR 3.2 0.6 - - - -
176B VAL* 1.3 83.1 - - + +
178B GLU* 1.3 56.8 + - - +
180B PHE* 2.9 34.4 + - + +
183B VAL* 3.7 40.3 - - + +
185B ILE* 3.7 31.4 - - + +
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Residues in contact with GLU 178 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167A LYS* 5.4 4.7 - - - -
174B LYS* 3.3 18.9 + - - +
175B TYR* 3.3 45.3 - - + +
177B LEU* 1.3 73.6 - - - +
179B ALA* 1.3 60.6 + - - +
180B PHE 3.1 8.8 + - - -
181B PRO* 4.6 4.3 - - - +
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Residues in contact with ALA 179 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121A ALA* 5.7 9.5 - - + +
122A THR 5.9 0.5 - - - -
123A PRO* 4.9 9.2 - - - +
134A TYR* 3.8 17.5 - - - +
175B TYR 5.0 1.1 - - - +
176B VAL 3.3 14.2 + - - +
177B LEU 3.2 0.4 - - - -
178B GLU* 1.3 81.2 - - + +
180B PHE* 1.3 72.3 + - + +
181B PRO* 3.7 8.8 - - - +
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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