Contacts of the helix formed by residues 158 - 173 (chain S) in PDB entry 5LN3
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 PRO 158 (chain S).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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156S SER 3.8 8.7 - - - +
157S THR* 1.4 91.6 - - - +
159S LEU* 1.4 63.6 + - - +
160S LEU 3.3 0.6 + - - -
161S PRO* 3.7 10.6 - - + +
162S GLU* 3.7 18.6 + - - +
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Residues in contact with LEU 159 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156S SER* 3.8 23.3 - - - +
157S THR 3.5 1.0 - - - -
158S PRO* 1.4 81.0 - - + +
160S LEU* 1.3 63.8 - - - +
162S GLU* 3.3 33.3 + - - +
163S VAL* 3.4 27.6 + - + +
198S GLN* 4.7 20.2 - - - +
201S ARG 5.8 1.6 - - - +
202S ALA* 4.9 12.8 - - + -
204S ASP* 3.9 29.4 - - + +
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Residues in contact with LEU 160 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156S SER 3.5 14.7 + - - +
157S THR* 4.6 0.9 - - - +
158S PRO 3.3 1.2 - - - -
159S LEU* 1.3 79.6 - - - +
161S PRO* 1.3 71.4 - - + +
163S VAL* 3.2 27.1 - - + +
164S GLU* 3.2 22.8 + - + +
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Residues in contact with PRO 161 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157S THR 3.3 24.2 - - - +
158S PRO* 3.7 7.2 - - + +
160S LEU* 1.3 89.2 - - + +
162S GLU* 1.4 63.0 + - - +
164S GLU* 3.8 13.4 - - + +
165S ALA* 3.1 23.0 + - - +
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Residues in contact with GLU 162 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158S PRO* 3.7 14.0 - - - +
159S LEU* 3.3 34.7 + - - +
161S PRO* 1.4 80.2 - - - +
163S VAL* 1.3 67.2 + - + +
165S ALA* 3.2 12.1 + - - +
166S TYR* 3.0 44.2 + - + +
198S GLN* 4.8 9.7 + - - -
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Residues in contact with VAL 163 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159S LEU* 3.4 29.8 - - + +
160S LEU* 3.2 31.4 - - + +
162S GLU* 1.3 85.2 - - + +
164S GLU* 1.4 55.2 + - - +
166S TYR* 3.0 20.1 + - + +
167S LEU* 2.9 40.8 + - + +
204S ASP 6.1 0.7 - - - +
205S LEU* 6.4 3.1 - - + -
206S VAL* 6.3 1.6 - - + -
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Residues in contact with GLU 164 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160S LEU* 3.2 29.8 + - + +
161S PRO* 3.9 11.2 - - - +
163S VAL* 1.4 73.7 - - + +
165S ALA* 1.4 59.8 + - - +
167S LEU* 3.1 14.3 + - + +
168S GLN* 2.8 53.0 + - + +
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Residues in contact with ALA 165 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161S PRO 3.1 13.5 + - - +
162S GLU* 3.2 12.3 - - - +
164S GLU* 1.4 74.4 - - - +
166S TYR* 1.3 66.2 + - + +
168S GLN* 3.3 16.9 + - - +
169S LEU* 2.9 29.5 + - - +
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Residues in contact with TYR 166 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162S GLU* 3.0 51.5 + - + +
163S VAL* 3.0 20.7 + - + +
165S ALA* 1.3 82.8 - - + +
167S LEU* 1.3 58.0 + - + +
169S LEU* 3.1 13.7 + - + +
170S LEU* 3.0 33.6 + - + +
191S LEU* 3.8 36.6 - - + +
194S LYS* 5.0 19.4 - - + +
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Residues in contact with LEU 167 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160S LEU* 6.5 0.4 - - + -
163S VAL* 2.9 30.5 + - + +
164S GLU* 3.4 13.7 - - + +
166S TYR* 1.3 74.5 - - + +
168S GLN* 1.4 62.3 + - + +
170S LEU* 3.3 23.1 + - + +
171S VAL* 3.4 18.0 + - - +
206S VAL* 3.8 31.0 - - + +
207S ALA* 6.4 0.2 - - - -
209S LYS* 4.2 29.4 - - + -
210S CYS* 5.9 1.1 - - - -
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Residues in contact with GLN 168 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164S GLU* 2.8 49.2 + - + +
165S ALA* 3.4 16.2 + - - +
167S LEU* 1.4 68.2 - - + +
169S LEU* 1.4 65.9 + - - +
171S VAL* 3.0 20.4 + - - +
172S VAL* 3.3 21.8 + - + +
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Residues in contact with LEU 169 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165S ALA 2.9 14.6 + - - +
166S TYR* 3.1 15.5 + - + +
168S GLN* 1.4 75.0 - - - +
170S LEU* 1.3 64.6 + - - +
172S VAL* 3.6 10.0 + - + +
173S ILE* 3.4 32.0 + - + +
187S ILE* 5.3 13.9 - - + -
190S ASP* 6.2 0.2 - - - +
191S LEU* 4.1 27.1 - - + -
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Residues in contact with LEU 170 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166S TYR* 3.0 23.1 + - + +
167S LEU* 3.6 24.5 - - + +
168S GLN 3.2 0.4 - - - -
169S LEU* 1.3 77.7 - - - +
171S VAL* 1.4 61.4 + - + +
173S ILE* 3.2 18.5 - - + +
174S PHE* 3.2 22.8 - - + -
188S SER* 3.6 29.2 - - - +
191S LEU* 4.3 11.7 - - + -
209S LYS* 4.9 0.9 - - + -
210S CYS* 3.5 34.8 - - - +
213S TYR* 4.2 32.3 - - + +
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Residues in contact with VAL 171 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167S LEU 3.4 15.7 + - - +
168S GLN* 3.0 12.4 + - - +
170S LEU* 1.4 74.9 - - + +
172S VAL* 1.3 64.2 + - + +
174S PHE* 3.5 22.1 + - - +
213S TYR* 5.3 9.6 - - - +
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Residues in contact with VAL 172 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168S GLN* 3.4 17.7 - - + +
169S LEU* 3.7 15.3 - - + +
171S VAL* 1.3 77.7 - - + +
173S ILE* 1.4 61.4 + - + +
174S PHE 3.1 11.2 + - - +
176S MET* 3.2 45.9 - - - +
177S ASN* 3.9 14.4 - - - +
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Residues in contact with ILE 173 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169S LEU* 3.4 25.1 + - + +
170S LEU* 3.2 24.9 - - + +
172S VAL* 1.4 74.6 - - + +
174S PHE* 1.3 63.2 + - + +
175S MET 3.4 1.3 + - - -
177S ASN* 3.6 33.8 - - + +
178S SER* 3.1 24.6 + - - -
184S ALA* 3.4 37.3 - - + +
187S ILE* 3.8 28.0 - - + -
188S SER* 4.3 11.2 - - - +
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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
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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