Contacts of the helix formed by residues 164 - 176 (chain D) in PDB entry 3LEE
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 SER 164 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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162D VAL* 3.8 2.1 - - - +
163D THR* 1.3 85.9 + - - +
165D GLU* 1.3 60.7 + - - +
166D GLN* 3.3 15.5 + - - +
167D GLU* 3.1 24.9 + - - +
168D TRP* 2.9 26.7 + - - +
232D PRO* 4.4 2.9 - - - -
234D GLU* 3.3 33.9 - - - -
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Residues in contact with GLU 165 (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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164D SER* 1.3 73.2 - - - +
166D GLN* 1.3 62.9 + - + +
168D TRP* 3.3 9.4 - - + +
169D ASP* 3.1 33.7 + - - +
232D PRO* 4.6 7.6 - - + +
234D GLU* 4.8 5.0 + - - +
235D VAL* 3.2 32.8 - - + +
238D ARG* 4.7 1.9 + - - -
261D GLU* 3.9 12.0 - - - +
262D LEU* 5.9 0.4 - - + +
265D ASN* 4.0 25.1 + - - +
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Residues in contact with GLN 166 (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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164D SER* 3.1 11.7 + - - +
165D GLU* 1.3 78.1 - - + +
167D GLU* 1.3 62.4 + - + +
169D ASP* 3.6 8.5 + - - +
170D LYS* 3.2 22.7 + - - +
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Residues in contact with GLU 167 (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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157D PHE* 3.5 27.1 - - + -
160D LYS* 3.7 20.2 + - - -
161D HIS 4.9 2.1 - - - +
162D VAL* 4.0 3.7 - - + +
163D THR* 3.7 22.5 + - - +
164D SER* 3.1 25.6 + - - +
166D GLN* 1.3 74.4 - - + +
168D TRP* 1.3 65.4 + - - +
169D ASP 3.2 0.4 - - - -
170D LYS* 3.4 31.4 + - - +
171D TYR* 3.0 24.3 + - - +
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Residues in contact with TRP 168 (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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162D VAL* 3.4 23.7 - - + +
164D SER 2.9 13.3 + - - +
165D GLU* 3.3 15.3 - - + +
167D GLU* 1.3 77.8 - - - +
169D ASP* 1.3 60.0 + - - +
171D TYR* 3.6 4.2 + + - +
172D CYS* 3.0 44.1 + - - -
213D LYS* 3.7 48.5 - - + -
216D ILE* 4.0 26.6 - - + +
217D ILE* 5.0 3.4 - - + -
230D PHE 3.7 15.0 + - - -
232D PRO* 4.0 27.6 - - + -
262D LEU* 4.2 27.1 - - + -
265D ASN* 3.4 34.8 - - + -
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Residues in contact with ASP 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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165D GLU 3.1 15.1 + - - +
166D GLN* 3.7 11.8 - - - +
167D GLU 3.2 0.2 - - - -
168D TRP* 1.3 77.8 - - - +
170D LYS* 1.3 59.6 + - - +
172D CYS* 3.7 1.8 + - - +
173D HIS* 2.9 30.2 + - - +
209D LEU* 4.0 19.1 - - + +
213D LYS* 2.7 35.4 + - - +
265D ASN* 4.9 2.6 + - - +
269D HIS* 4.9 3.3 + - - -
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Residues in contact with LYS 170 (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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156D GLU* 2.9 29.7 + - - -
157D PHE* 4.5 3.4 - - + -
160D LYS* 5.3 0.2 - - - +
166D GLN 3.2 12.5 + - - +
167D GLU* 3.3 33.1 + - - +
169D ASP* 1.3 79.1 - - - +
171D TYR* 1.3 63.3 + - - +
173D HIS* 3.1 12.0 - - + +
174D TYR* 3.0 62.5 + - + -
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Residues in contact with TYR 171 (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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83D GLU* 3.7 18.8 + - - -
153D GLY 5.4 1.8 - - - -
154D MET* 5.8 4.5 - - + -
157D PHE* 3.4 53.8 - + + -
162D VAL* 4.6 13.7 - - + -
167D GLU 3.0 12.6 + - - +
168D TRP* 3.8 7.9 - + - +
170D LYS* 1.3 72.0 - - - +
172D CYS* 1.3 73.6 + - - +
173D HIS 2.9 5.4 + - - -
174D TYR* 2.9 17.5 + - + +
175D VAL* 2.9 38.4 + - + +
212D GLN* 5.5 1.1 - - - -
216D ILE* 4.9 9.4 - - + -
230D PHE* 3.4 38.9 - + + -
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Residues in contact with CYS 172 (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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168D TRP* 3.0 46.5 + - - +
169D ASP* 4.1 0.9 - - - +
171D TYR* 1.3 80.5 - - - +
173D HIS* 1.3 49.9 + - - +
175D VAL* 4.0 10.8 - - - -
176D ALA* 3.2 8.9 + - - +
177D GLY 2.5 30.3 + - - -
209D LEU* 3.2 25.5 - - + +
212D GLN* 3.9 21.1 - - + -
213D LYS* 4.2 16.2 - - - -
216D ILE* 4.2 4.9 - - - -
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Residues in contact with HIS 173 (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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149D ARG* 5.2 4.8 + - - -
169D ASP 2.9 14.7 + - - +
170D LYS* 3.1 16.8 - - + +
171D TYR 2.9 0.6 + - - -
172D CYS* 1.3 76.2 - - - +
174D TYR* 1.3 79.6 + + - +
177D GLY 3.1 0.8 + - - +
178D LEU* 2.7 59.7 + - + +
181D ILE* 4.3 8.5 - - + -
205D ASN* 2.4 36.1 + - - +
209D LEU* 3.5 8.5 - - + -
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Residues in contact with TYR 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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149D ARG* 3.8 15.9 - - + -
150D MET* 3.1 29.7 - - - +
152D ILE* 4.3 8.1 - - + +
153D GLY* 3.5 47.1 - - - +
154D MET* 4.7 3.4 - - + +
156D GLU* 3.3 11.3 + - - -
157D PHE* 4.3 10.1 - + - -
170D LYS* 3.0 58.2 + - + -
171D TYR* 2.9 8.5 + - + +
173D HIS* 1.3 93.7 - + - +
175D VAL* 1.3 63.2 + - + +
176D ALA 3.3 0.3 + - - -
178D LEU* 3.5 14.5 - - + +
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Residues in contact with VAL 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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80D ASP* 5.5 1.8 - - - +
83D GLU* 3.8 9.9 - - - +
150D MET* 4.1 12.2 - - + +
154D MET* 3.6 30.7 - - + -
171D TYR* 2.9 41.7 + - + +
172D CYS* 4.0 5.2 - - - -
174D TYR* 1.3 78.1 - - + +
176D ALA* 1.3 60.4 + - + +
179D VAL* 4.1 10.7 - - - +
212D GLN* 2.9 32.5 + - + +
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Residues in contact with ALA 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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172D CYS 3.2 9.2 + - - +
174D TYR 3.2 1.0 - - - -
175D VAL* 1.3 78.2 - - - +
177D GLY* 1.3 69.7 + - - +
178D LEU 3.3 1.3 - - - -
179D VAL* 3.2 12.3 + - - +
180D GLY 3.2 13.9 + - - -
208D GLY* 3.7 15.0 - - - +
212D GLN* 3.2 43.7 - - + +
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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