Contacts of the helix formed by residues 160 - 183 (chain D) in PDB entry 4LEY
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 LYS 160 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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155D ASP 5.7 3.1 - - - -
156D LYS 5.6 3.4 - - - -
158D ARG 4.1 12.6 - - - +
159D LEU* 1.3 76.2 - - - +
161D ARG* 1.3 65.5 + - - +
162D LYS* 3.3 6.1 - - + +
163D ASP* 3.3 32.2 + - - +
164D ILE* 3.1 25.1 + - - +
207D SER 5.5 3.8 - - - +
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Residues in contact with ARG 161 (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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159D LEU 4.1 1.0 + - - -
160D LYS* 1.3 71.7 - - - +
162D LYS* 1.3 63.8 + - - +
164D ILE* 3.1 13.1 + - + +
165D SER* 2.9 31.9 + - - +
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Residues in contact with LYS 162 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160D LYS* 3.3 4.6 - - + +
161D ARG* 1.3 78.9 - - - +
163D ASP* 1.3 71.0 + - - +
165D SER* 3.3 4.5 + - - -
166D GLU* 2.3 73.0 + - + +
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Residues in contact with ASP 163 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160D LYS* 3.3 38.0 + - + +
162D LYS* 1.3 83.4 + - - +
164D ILE* 1.3 56.8 + - - +
166D GLU* 3.8 11.2 - - - +
167D ALA* 2.9 32.6 + - - +
207D SER 5.4 3.1 - - - +
208D ALA* 5.7 1.6 - - - +
209D PRO* 4.0 21.8 - - + +
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Residues in contact with ILE 164 (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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159D LEU* 3.7 31.9 - - + +
160D LYS 3.1 20.9 + - - +
161D ARG* 3.1 13.2 + - + +
163D ASP* 1.3 73.4 - - - +
165D SER* 1.3 62.1 + - - +
167D ALA* 3.9 0.3 - - - +
168D ALA* 2.9 36.6 + - + +
200D TYR* 3.4 25.6 + - + +
209D PRO* 4.0 22.0 - - + -
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Residues in contact with SER 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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161D ARG* 2.9 20.7 + - - +
162D LYS* 3.9 4.8 - - - -
164D ILE* 1.3 78.8 - - - +
166D GLU* 1.3 65.4 + - - +
168D ALA* 4.7 2.7 - - - -
169D GLU* 3.0 31.0 + - - +
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Residues in contact with GLU 166 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162D LYS* 2.3 66.5 + - + +
163D ASP* 3.8 9.8 - - - +
165D SER* 1.3 79.7 - - - +
167D ALA* 1.3 61.3 + - - +
169D GLU* 4.1 7.5 - - - +
170D THR* 3.6 19.1 + - - -
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Residues in contact with ALA 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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163D ASP 2.9 19.2 + - - +
164D ILE 3.9 2.2 - - - +
166D GLU* 1.3 74.8 - - - +
168D ALA* 1.3 66.6 + - - +
169D GLU 3.2 0.7 + - - -
170D THR* 3.3 5.7 + - - -
171D VAL* 3.0 28.7 + - + +
209D PRO* 3.7 30.7 - - + +
212D PHE* 4.0 6.5 - - + -
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Residues in contact with ALA 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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164D ILE* 2.9 24.1 + - + +
165D SER* 4.2 2.9 - - - +
167D ALA* 1.3 73.7 - - - +
169D GLU* 1.3 58.0 + - - +
171D VAL* 4.3 6.7 - - - -
172D ASN* 2.9 45.7 + - - +
200D TYR* 3.7 22.2 - - + +
212D PHE* 4.3 6.2 - - + -
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Residues in contact with GLU 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 SER* 3.0 21.8 + - - +
166D GLU* 4.1 8.5 - - - +
167D ALA 3.2 0.2 - - - -
168D ALA* 1.3 77.0 - - - +
170D THR* 1.3 64.5 + - - +
172D ASN* 3.6 5.8 - - - +
173D LYS* 3.0 44.8 + - - +
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Residues in contact with THR 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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166D GLU 3.6 10.3 + - - -
167D ALA* 3.3 7.9 + - - -
169D GLU* 1.3 78.5 - - - +
171D VAL* 1.3 67.0 + - + +
173D LYS* 3.0 16.2 + - + +
174D VAL* 3.0 37.2 + - + +
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Residues in contact with VAL 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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167D ALA* 3.0 21.9 + - + +
168D ALA* 3.9 6.1 - - - +
170D THR* 1.3 79.5 - - + +
172D ASN* 1.3 64.5 + - - +
174D VAL* 3.3 5.8 + - - +
175D VAL* 2.9 47.6 + - + +
201D TYR* 4.9 3.8 - - - +
212D PHE* 3.6 51.6 - - + -
214D VAL* 5.5 0.7 - - + -
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Residues in contact with ASN 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 ALA* 2.9 34.6 + - - +
169D GLU* 3.6 5.4 - - - +
171D VAL* 1.3 78.9 - - - +
173D LYS* 1.3 66.8 + - - +
175D VAL* 3.9 6.2 - - - +
176D GLU* 2.9 28.2 + - - +
194D GLN* 5.7 2.6 + - - -
196D ASN* 5.8 1.2 + - - -
201D TYR* 4.6 9.2 + - - -
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Residues in contact with LYS 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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169D GLU* 3.0 38.9 + - + +
170D THR* 3.2 15.9 - - + +
172D ASN* 1.3 76.3 - - - +
174D VAL* 1.3 64.8 + - + +
176D GLU* 3.3 7.9 + - - +
177D ARG* 3.0 23.8 + - - +
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Residues in contact with VAL 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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170D THR* 3.0 27.7 + - + +
171D VAL* 3.7 8.1 - - - +
173D LYS* 1.3 77.1 - - + +
175D VAL* 1.3 64.0 + - + +
177D ARG* 3.1 7.6 + - - +
178D LEU* 3.0 44.5 + - + +
274D VAL* 5.4 4.3 - - + -
277D ILE* 4.2 26.2 - - + -
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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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171D VAL* 2.9 39.7 + - + +
172D ASN* 3.9 7.6 - - - +
174D VAL* 1.3 73.6 - - + +
176D GLU* 1.3 59.4 + - - +
178D LEU* 3.4 9.9 + - + +
179D LEU* 2.9 28.7 + - + +
194D GLN* 3.6 34.3 - - - +
214D VAL* 4.1 27.6 - - + -
216D PHE* 4.2 9.4 - - + -
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Residues in contact with GLU 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 ASN 2.9 20.4 + - - +
173D LYS* 3.5 7.8 - - - +
175D VAL* 1.3 77.6 - - - +
177D ARG* 1.3 59.0 + - - +
179D LEU* 3.7 8.6 - - + +
180D ARG* 2.9 49.8 + - - +
194D GLN* 5.9 0.4 - - - -
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Residues in contact with ARG 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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173D LYS 3.0 13.2 + - - +
174D VAL* 3.1 10.0 + - - +
176D GLU* 1.3 78.2 - - - +
178D LEU* 1.3 63.2 + - - +
180D ARG* 3.2 9.4 + - - +
181D ARG* 2.9 22.5 + - - +
273D GLU* 3.0 31.2 + - + +
276D GLU* 3.5 26.8 + - - +
277D ILE* 3.8 42.9 - - + +
278D LYS 5.0 1.2 - - - +
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Residues in contact with LEU 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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174D VAL* 3.0 33.4 + - + +
175D VAL* 3.9 7.2 - - + +
177D ARG* 1.3 74.4 - - - +
179D LEU* 1.3 64.8 + - - +
181D ARG* 3.2 8.4 + - - +
182D MET* 2.9 26.8 + - + +
216D PHE* 4.2 14.4 - - + -
270D ILE* 4.2 30.1 - - + +
273D GLU* 3.7 28.9 - - + -
274D VAL* 4.0 22.0 - - + +
277D ILE* 5.0 3.1 - - + -
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Residues in contact with LEU 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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175D VAL* 2.9 18.6 + - + +
176D GLU* 3.7 7.9 - - + +
178D LEU* 1.3 75.5 - - - +
180D ARG* 1.3 62.0 + - - +
182D MET* 3.0 10.4 + - - +
183D GLN* 2.7 38.5 - - - +
192D VAL* 3.8 31.9 - - + +
193D GLU* 5.9 0.2 - - - -
194D GLN* 3.9 33.4 - - + +
216D PHE* 3.8 23.7 - - + -
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Residues in contact with ARG 180 (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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176D GLU* 2.9 39.4 + - + +
177D ARG* 3.4 8.7 - - + +
179D LEU* 1.3 77.1 - - - +
181D ARG* 1.3 62.9 + - - +
183D GLN* 3.3 10.8 + - - +
184D LYS* 3.3 47.3 - - + +
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Residues in contact with ARG 181 (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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177D ARG 2.9 12.3 + - - +
178D LEU 3.3 9.6 - - - +
180D ARG* 1.3 75.6 - - - +
182D MET* 1.3 64.5 + - + +
184D LYS* 3.1 28.4 + - - +
185D ARG* 3.2 51.4 - - - +
187D SER* 4.7 3.4 - - - -
269D ILE* 3.5 46.8 + - + +
272D GLU* 3.6 21.2 + - - +
273D GLU* 3.2 42.8 + - + +
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Residues in contact with MET 182 (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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178D LEU* 2.9 17.3 + - + +
179D LEU* 3.0 14.5 + - - +
181D ARG* 1.3 77.9 - - + +
183D GLN* 1.3 60.4 + - - +
184D LYS 3.3 0.4 - - - -
187D SER* 3.0 23.8 + - - -
189D PHE* 3.4 42.2 - - + +
190D LYS* 3.2 12.1 + - - -
192D VAL* 4.3 10.1 - - + -
216D PHE* 4.2 10.5 - - + -
266D PHE* 3.7 32.1 - - + +
269D ILE* 4.1 22.7 - - + -
270D ILE* 3.9 24.9 - - + -
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Residues in contact with GLN 183 (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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179D LEU* 2.7 40.7 + - - +
180D ARG* 3.3 8.0 + - - +
181D ARG 3.2 1.0 - - - -
182D MET* 1.3 79.6 - - - +
184D LYS* 1.3 63.8 + - + +
185D ARG 5.2 0.5 - - - +
190D LYS* 3.5 30.8 + - + +
191D GLY* 3.4 22.4 - - - +
192D VAL* 2.2 42.3 + - - +
193D GLU* 5.1 2.0 - - - +
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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
------------------------------------------------------------
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