Contacts of the helix formed by residues 163 - 179 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1D UNL 4.5 11.7 - - - -
71D ARG* 5.8 3.4 - - - +
95D LEU* 3.8 29.4 - - + -
96D GLY* 3.6 24.2 - - - +
97D ASN* 4.6 0.9 - - - +
119D ASP 6.6 0.4 - - - -
160D PHE* 2.8 36.3 + - + +
161D TYR 3.9 0.9 - - - -
162D SER* 1.3 81.9 - - - +
164D PRO* 1.4 60.3 - - + +
165D VAL* 4.0 14.6 - - + +
166D CYS* 2.8 27.5 + - + +
167D LYS 3.0 9.4 + - - -
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Residues in contact with PRO 164 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96D GLY 4.1 8.5 - - - +
98D LEU* 3.8 33.4 - - + -
119D ASP 4.4 2.0 - - - +
120D THR* 4.6 7.4 - - + -
121D ALA* 4.0 33.4 - - + +
162D SER 3.3 11.4 - - - +
163D VAL* 1.4 84.3 - - + -
165D VAL* 1.3 57.7 + - - +
167D LYS* 3.3 13.3 - - + +
168D ILE* 3.1 34.2 + - + +
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Residues in contact with VAL 165 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1D UNL 4.3 5.6 - - + +
95D LEU* 4.4 1.6 - - + -
119D ASP* 3.3 47.3 - - + +
121D ALA* 6.1 0.4 - - + -
130D THR* 3.9 2.0 - - + +
133D ASN* 3.4 28.4 - - - +
163D VAL* 3.1 16.9 + - + +
164D PRO* 1.3 75.5 - - - +
166D CYS* 1.3 63.6 + - - +
168D ILE* 3.5 11.6 + - + +
169D ARG* 3.1 55.4 + - - +
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Residues in contact with CYS 166 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1D UNL 4.3 17.3 - - - -
158D ASN* 5.3 1.9 - - - +
160D PHE* 3.3 33.0 - - - +
161D TYR* 4.6 2.6 - - - +
163D VAL* 2.8 4.9 + - + +
165D VAL* 1.3 80.1 - - - +
167D LYS* 1.3 60.5 + - - +
169D ARG* 3.4 7.5 + - - +
170D TYR* 2.9 31.5 + - - +
224D CYS* 2.0 56.3 - - - +
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Residues in contact with LYS 167 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175C TYR* 4.1 10.0 + - - +
178C GLU* 5.9 0.6 + - - -
161D TYR* 3.3 64.0 + - + +
163D VAL 3.0 6.7 + - - +
164D PRO* 3.3 17.3 - - + +
166D CYS* 1.3 77.1 - - - +
168D ILE* 1.3 66.4 + - + +
170D TYR* 3.7 0.7 - - - +
171D ASP* 3.0 43.0 + - - +
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Residues in contact with ILE 168 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175C TYR* 3.5 16.6 - - + +
121D ALA* 5.3 11.7 - - + -
133D ASN* 3.5 36.3 - - + +
134D TYR* 3.7 47.6 - - + +
164D PRO* 3.1 23.0 + - + +
165D VAL* 3.8 12.1 - - + +
166D CYS 3.3 0.2 - - - -
167D LYS* 1.3 78.2 - - + +
169D ARG* 1.3 56.1 + - - +
171D ASP* 3.8 0.7 - - - +
172D GLN* 2.9 32.9 + - + +
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Residues in contact with ARG 169 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1D UNL 2.8 42.2 + - - -
119D ASP* 4.6 0.2 + - - -
133D ASN* 2.9 42.3 + - + +
136D ILE* 4.6 0.4 - - + +
137D GLY* 4.2 20.1 - - - +
165D VAL* 3.1 32.5 + - - +
166D CYS* 3.8 9.0 - - - +
167D LYS 3.3 0.2 - - - -
168D ILE* 1.3 77.0 - - - +
170D TYR* 1.3 61.3 + - - +
172D GLN* 3.7 1.6 + - - +
173D MET* 3.1 18.0 + - - +
222D TRP* 3.5 22.5 - - + -
224D CYS* 2.5 42.8 + - + -
249D VAL* 3.6 24.2 - - + +
272D GLN* 3.6 8.3 + - - +
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Residues in contact with TYR 170 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187B GLU* 3.8 28.3 - - + -
188B PRO* 3.4 10.6 - - - +
156D VAL* 4.2 7.2 - - + -
158D ASN* 3.6 30.1 - - + +
161D TYR* 3.4 25.1 - + + -
166D CYS 2.9 17.5 + - - +
167D LYS 3.7 2.5 - - - +
169D ARG* 1.3 74.3 - - - +
171D ASP* 1.3 59.5 + - - +
173D MET* 3.0 10.9 + - + +
174D LYS* 2.8 67.9 + - + +
189D GLU* 2.8 29.8 + - - -
222D TRP* 3.7 24.5 - + + -
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Residues in contact with ASP 171 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187B GLU* 4.7 3.3 - - - +
175C TYR* 2.7 43.7 + - + +
161D TYR* 2.9 26.3 + - - -
167D LYS* 3.0 30.3 + - - +
168D ILE 3.8 0.2 - - - +
170D TYR* 1.3 81.0 - - - +
172D GLN* 1.3 58.2 + - - +
174D LYS* 3.5 7.6 + - - +
175D TYR* 2.9 29.6 + - - +
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Residues in contact with GLN 172 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134C TYR* 4.7 1.6 + - - +
172C GLN* 3.1 42.9 + - - +
175C TYR* 3.9 18.1 - - + +
133D ASN 4.4 0.7 - - - +
134D TYR* 3.1 39.5 + - - +
137D GLY* 3.7 6.1 - - - -
138D ALA* 3.6 26.6 - - - +
168D ILE* 2.9 25.0 + - + +
171D ASP* 1.3 73.5 - - - +
173D MET* 1.3 61.3 + - - +
175D TYR* 3.4 7.7 + - - +
176D VAL* 3.0 34.3 + - - +
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Residues in contact with MET 173 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137D GLY 4.3 2.4 + - - +
141D ALA* 3.6 24.0 - - + -
144D MET* 4.2 22.2 - - - -
156D VAL* 4.4 10.8 - - + -
169D ARG 3.1 12.2 + - - +
170D TYR* 3.0 19.1 + - + +
172D GLN* 1.3 77.2 - - - +
174D LYS* 1.3 71.5 + - + +
176D VAL* 3.6 0.9 + - - +
177D LEU* 3.0 43.5 + - + +
185D ILE* 3.4 33.2 - - + -
222D TRP* 3.8 37.5 - - + +
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Residues in contact with LYS 174 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187B GLU* 3.1 23.9 + - - +
188B PRO* 3.7 15.8 - - - +
189B GLU* 4.3 5.3 + - - +
170D TYR* 2.8 47.8 + - + +
171D ASP* 3.7 9.0 - - - +
173D MET* 1.3 84.4 - - + +
175D TYR* 1.3 62.2 + - - +
177D LEU* 3.3 11.8 + - - +
178D GLU* 3.3 22.9 + - + +
185D ILE* 3.7 28.7 - - + -
189D GLU* 4.5 0.7 - - - -
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Residues in contact with TYR 175 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134C TYR* 3.6 41.0 + + - -
167C LYS* 3.7 12.3 + - - -
168C ILE* 3.5 24.0 + - + +
171C ASP* 2.6 45.5 + - + +
172C GLN* 3.9 15.5 - - - -
171D ASP 2.9 19.1 + - - +
172D GLN* 3.4 10.1 + - - +
174D LYS* 1.3 73.6 - - - +
176D VAL* 1.3 64.7 - - - +
178D GLU* 3.2 45.7 + - - +
179D ALA* 4.1 1.9 + - - +
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Residues in contact with VAL 176 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134C TYR* 4.0 30.2 + - + +
138D ALA* 3.9 24.2 - - - +
141D ALA* 3.9 18.8 - - + -
142D LEU* 4.0 28.3 - - + +
145D VAL* 4.3 8.1 - - + -
172D GLN* 3.0 20.8 + - - +
173D MET 3.8 4.3 - - - +
175D TYR* 1.3 75.1 - - - +
177D LEU* 1.3 68.1 + - + +
179D ALA* 3.2 15.4 + - - +
180D PHE* 3.4 15.1 - - + -
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Residues in contact with LEU 177 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141D ALA* 4.7 3.1 - - + -
144D MET* 4.5 13.5 - - + -
145D VAL* 3.9 26.9 - - + -
154D VAL* 4.7 7.6 - - + -
173D MET* 3.0 47.1 + - + +
174D LYS* 3.7 7.0 - - - +
175D TYR 3.2 0.8 - - - -
176D VAL* 1.3 78.4 - - + +
178D GLU* 1.3 61.8 + - - +
179D ALA 3.3 0.2 - - - -
180D PHE* 3.0 30.1 + - - +
181D PRO* 5.1 0.2 - - - +
183D VAL* 3.9 33.4 - - + +
185D ILE* 3.8 22.0 - - + -
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Residues in contact with GLU 178 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167C LYS* 5.3 4.2 + - - -
174D LYS* 3.3 18.9 + - + +
175D TYR* 3.4 39.6 - - - +
176D VAL 3.2 0.2 - - - -
177D LEU* 1.3 73.4 - - - +
179D ALA* 1.3 56.6 + - - +
180D PHE* 3.0 11.6 + - - -
181D PRO* 4.4 4.7 - - - +
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Residues in contact with ALA 179 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121C ALA* 5.5 11.9 - - + -
122C THR 5.8 0.7 - - - -
123C PRO* 5.1 9.1 - - - +
134C TYR* 3.8 18.6 - - - +
175D TYR 4.1 1.5 + - - +
176D VAL 3.2 13.1 + - - +
178D GLU* 1.3 76.7 - - - +
180D PHE* 1.3 73.9 + - + +
181D PRO* 3.6 9.2 - - - +
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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
------------------------------------------------------------
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