Contacts of the helix formed by residues 159 - 177 (chain B) in PDB entry 5D1L
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 CYS 159 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147B ALA* 3.3 10.0 + - - +
148B PHE* 3.6 33.0 - - - -
149B THR* 3.9 11.7 - - - -
157B PHE 3.5 0.8 + - - -
158B HIS* 1.3 72.0 - - - +
160B HIS* 1.3 62.1 + - - +
162B LEU* 3.5 1.6 + - - +
163B ALA* 3.1 24.1 + - - +
211B SER 5.8 0.2 - - - -
212B LEU* 3.7 30.3 - - + +
215B ALA* 3.5 30.1 - - + -
216B PRO 5.8 0.2 - - - +
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Residues in contact with HIS 160 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158B HIS* 3.3 1.0 - - + +
159B CYS* 1.3 77.3 - - - +
161B CYS* 1.3 74.6 + - - +
163B ALA* 3.4 7.7 + - - +
164B ARG* 3.3 49.0 + - + +
212B LEU 4.3 3.6 + - - -
213B LYS* 6.0 1.1 - - - +
215B ALA* 5.3 5.1 + - - +
216B PRO 5.0 3.0 + - - +
217B GLU* 3.6 47.9 + - + +
218B PRO* 4.2 19.5 - - + +
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Residues in contact with CYS 161 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A PHE* 5.5 0.4 - - - -
135B CYS* 3.9 3.1 - - - -
137B ILE* 3.6 32.1 - - + +
138B CYS* 3.7 16.6 - - - -
158B HIS* 3.2 14.3 + - - +
160B HIS* 1.3 91.6 - - - +
162B LEU* 1.3 61.4 + - - +
164B ARG* 3.3 7.7 + - - +
165B ALA 3.2 16.5 + - - -
218B PRO* 5.8 2.5 - - - -
220B GLN* 5.8 0.9 - - - -
301B ZN 2.4 37.2 - - - -
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Residues in contact with LEU 162 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137B ILE* 4.0 5.7 - - + +
149B THR* 4.0 24.9 - - + -
151B THR* 4.5 7.4 - - + -
157B PHE* 4.0 31.6 - - + +
158B HIS 3.1 11.3 + - - +
159B CYS 4.1 3.1 - - - +
161B CYS* 1.3 75.7 - - - +
163B ALA* 1.3 66.5 + - - +
165B ALA* 3.3 7.6 + - + +
166B ILE* 3.1 33.4 + - + +
169B MET* 5.8 0.2 - - + -
199B PRO* 4.5 12.8 - - + -
205B LEU* 4.1 28.0 - - + -
207B TYR* 5.9 1.1 - - + -
212B LEU* 4.1 16.4 - - + -
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Residues in contact with ALA 163 (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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159B CYS 3.1 18.3 + - - +
160B HIS* 3.6 7.0 - - - +
161B CYS 3.3 0.2 - - - -
162B LEU* 1.3 77.6 - - - +
164B ARG* 1.3 62.9 + - + +
166B ILE* 3.3 0.6 + - - -
167B GLN* 3.1 29.1 + - - +
209B LEU* 3.6 15.4 - - + +
212B LEU* 4.1 13.8 - - + +
213B LYS* 4.0 30.7 - - + +
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Residues in contact with ARG 164 (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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2A ALA 4.7 16.0 - - - +
59A ASP* 5.4 8.9 + - - +
60A TYR 5.2 4.0 + - - -
61A PRO* 5.4 1.8 - - - +
62A PHE* 3.5 43.1 - - + -
160B HIS* 3.3 37.0 + - + +
161B CYS* 3.7 6.2 - - - +
162B LEU 3.3 0.6 - - - -
163B ALA* 1.3 80.5 - - + +
165B ALA* 1.3 61.9 + - - +
167B GLN* 3.3 19.6 + - - +
168B HIS* 3.3 34.9 + - - -
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Residues in contact with ALA 165 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A PHE* 3.5 21.8 - - + -
95A PRO* 4.5 6.5 - - + -
137B ILE* 4.1 15.0 - - + -
161B CYS 3.2 10.5 + - - +
162B LEU* 3.3 10.9 + - + +
164B ARG* 1.3 78.0 - - - +
166B ILE* 1.3 62.3 + - - +
168B HIS* 3.4 4.5 + - - +
169B MET* 3.2 37.8 + - + +
199B PRO* 4.4 9.9 - - + -
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Residues in contact with ILE 166 (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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162B LEU* 3.1 38.2 + - + +
163B ALA 3.7 4.0 - - - +
165B ALA* 1.3 73.2 - - - +
167B GLN* 1.3 66.1 + - - +
169B MET* 3.2 10.6 + - + +
170B GLU* 3.0 31.3 + - + +
196B VAL* 4.2 13.5 - - + -
205B LEU* 4.2 9.9 - - + -
207B TYR* 3.5 62.6 - - + +
209B LEU* 4.1 11.2 - - + -
212B LEU* 4.0 10.3 - - + -
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Residues in contact with GLN 167 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163B ALA* 3.1 14.1 + - - +
164B ARG* 3.3 26.5 + - - +
166B ILE* 1.3 77.7 - - - +
168B HIS* 1.3 67.3 + - + +
170B GLU* 3.4 10.1 + - - +
171B GLN* 3.3 20.8 + - - +
209B LEU* 4.0 15.9 - - + -
213B LYS* 2.8 33.1 + - - -
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Residues in contact with HIS 168 (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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59A ASP* 3.6 30.5 + - + +
62A PHE* 3.4 42.1 - + + +
63A LYS* 3.2 31.9 - - + +
164B ARG* 3.3 28.0 + - - -
165B ALA 3.8 6.7 - - - +
166B ILE 3.3 0.6 - - - -
167B GLN* 1.3 83.7 - - + +
169B MET* 1.3 62.4 + - + +
171B GLN* 3.3 8.6 + - + +
172B GLU* 3.2 32.2 + - - +
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Residues in contact with MET 169 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95A PRO* 6.2 2.2 - - + -
162B LEU* 5.8 0.2 - - + -
165B ALA* 3.2 34.7 + - + +
166B ILE* 3.2 16.8 + - + +
168B HIS* 1.3 77.7 - - + +
170B GLU* 1.3 62.2 + - - +
172B GLU* 3.3 14.9 + - - +
173B LEU* 3.1 32.3 + - + +
195B GLY 4.9 1.6 - - - +
196B VAL* 4.0 22.2 - - + -
197B GLN* 3.3 48.5 - - - +
199B PRO* 4.7 8.3 - - + -
205B LEU* 5.5 1.6 - - + -
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Residues in contact with GLU 170 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166B ILE* 3.0 25.3 + - + +
167B GLN* 3.7 6.6 - - - +
168B HIS 3.3 0.2 - - - -
169B MET* 1.3 77.2 - - - +
171B GLN* 1.3 60.4 + - - +
173B LEU* 3.6 6.0 + - - +
174B LYS* 3.3 22.7 + - - +
194B VAL* 6.4 1.1 - - + -
196B VAL* 4.0 10.5 - - + -
207B TYR* 2.6 39.0 + - - +
209B LEU* 4.3 16.4 - - - +
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Residues in contact with GLN 171 (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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63A LYS* 3.0 32.3 + - - +
167B GLN 3.3 11.0 + - - +
168B HIS* 3.5 9.2 - - + +
169B MET 3.3 0.2 - - - -
170B GLU* 1.3 78.8 - - - +
172B GLU* 1.3 73.8 + - - +
174B LYS* 3.4 6.7 + - - +
175B ALA* 3.3 29.4 + - - +
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Residues in contact with GLU 172 (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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62A PHE 4.1 10.7 - - - +
63A LYS* 3.0 24.9 + - - +
168B HIS* 3.2 19.2 + - - +
169B MET* 3.3 15.0 + - - +
171B GLN* 1.3 91.3 - - - +
173B LEU* 1.3 68.2 + - + +
175B ALA* 3.3 4.4 + - - +
176B GLN* 3.1 30.6 + - + +
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Residues in contact with LEU 173 (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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169B MET* 3.1 22.5 + - + +
170B GLU* 3.8 6.3 - - - +
171B GLN 3.3 0.2 - - - -
172B GLU* 1.3 79.7 - - + +
174B LYS* 1.3 63.8 + - - +
176B GLN* 3.3 10.6 + - + +
177B GLY* 3.2 18.5 + - - -
194B VAL* 5.0 7.6 - - + -
195B GLY* 3.5 47.3 - - - +
196B VAL* 3.7 12.8 - - + +
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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
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170B GLU 3.3 13.8 + - - +
171B GLN* 3.8 7.0 - - - +
172B GLU 3.3 0.4 - - - -
173B LEU* 1.3 80.7 - - - +
175B ALA* 1.3 60.6 + - - +
176B GLN 3.2 0.9 + - - -
177B GLY 3.4 22.3 + - - +
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Residues in contact with ALA 175 (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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171B GLN* 3.3 26.6 + - - +
172B GLU* 3.8 5.4 - - - +
173B LEU 3.3 0.4 - - - -
174B LYS* 1.3 78.8 - - - +
176B GLN* 1.3 68.7 + - - +
177B GLY 5.0 0.7 - - - +
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Residues in contact with GLN 176 (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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172B GLU* 3.1 20.4 - - + +
173B LEU* 3.3 11.0 + - + +
174B LYS 3.2 0.8 - - - -
175B ALA* 1.3 88.8 - - - +
177B GLY* 1.3 59.9 + - - +
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Residues in contact with GLY 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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173B LEU 3.2 10.0 + - - -
174B LYS* 3.4 17.3 - - - +
175B ALA 5.0 0.9 - - - +
176B GLN* 1.3 81.8 - - - +
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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