Contacts of the helix formed by residues 163 - 173 (chain H) in PDB entry 3JSX
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 ASP 163 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169F TRP* 4.8 1.2 + - - -
256F GLY* 3.0 14.2 + - - +
258F HIS* 3.2 31.8 + - - +
155H TYR 3.9 5.9 - - - +
156H SER 3.9 5.2 + - - -
157H LEU* 3.8 20.4 - - + +
162H GLY* 1.3 70.6 - - - -
164H MET* 1.3 70.0 + - - +
165H ASN* 2.7 45.0 + - - +
166H VAL* 3.2 26.6 + - + +
167H ILE* 3.5 8.0 + - - +
263H ILE* 4.9 5.0 - - - +
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Residues in contact with MET 164 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103H LEU* 5.1 10.8 - - + -
146H ILE* 4.4 7.9 - - + -
148H THR* 6.5 0.9 - - - -
155H TYR* 3.3 29.0 + - + +
162H GLY 3.3 4.5 + - - -
163H ASP* 1.3 73.2 + - - +
165H ASN* 1.3 66.6 + - - +
166H VAL 3.1 0.7 - - - -
167H ILE* 3.2 28.1 + - + -
168H LEU* 3.0 50.2 + - + +
188H LEU* 3.4 32.1 - - + -
190H TYR* 3.7 25.8 - - + +
269H ILE* 4.2 9.9 - - + -
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Residues in contact with ASN 165 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157H LEU* 5.2 3.0 - - - +
163H ASP* 2.7 36.0 + - - +
164H MET* 1.3 78.9 - - - +
166H VAL* 1.3 58.9 + - - +
168H LEU* 3.4 2.4 + - - -
169H TRP* 3.2 19.2 + - - +
255H VAL* 4.1 13.9 - - + +
263H ILE* 5.6 1.3 - - + -
266H ASP* 3.3 32.5 + - - +
267H ASN 4.3 1.3 - - - -
268H GLN* 3.0 46.0 + - + +
269H ILE* 3.2 22.1 + - - +
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Residues in contact with VAL 166 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166F VAL* 4.0 18.5 - - + +
169F TRP* 3.0 39.7 - - + +
170F PRO* 4.4 0.9 - - - +
255F VAL* 3.7 25.8 - - + +
256F GLY* 4.5 1.3 - - - -
258F HIS* 4.4 4.9 - - + +
163H ASP* 3.3 28.9 - - + +
164H MET 3.1 0.2 - - - -
165H ASN* 1.3 74.5 - - - +
167H ILE* 1.3 63.4 + - - +
168H LEU 3.2 0.2 + - - -
169H TRP* 3.3 5.4 + - - +
170H PRO* 3.2 19.1 - - - +
255H VAL* 4.3 17.0 - - + -
263H ILE* 5.0 3.1 - - + -
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Residues in contact with ILE 167 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169F TRP* 4.5 14.1 - - + +
170F PRO* 4.1 11.6 - - + +
103H LEU* 4.4 10.5 - - + -
106H PHE* 3.1 65.2 - - + +
155H TYR* 3.8 22.2 - - + -
161H HIS 4.7 8.1 - - - +
163H ASP 3.5 10.7 + - - +
164H MET* 3.2 21.6 + - + +
166H VAL* 1.3 79.4 - - - +
168H LEU* 1.3 58.4 + - + +
170H PRO* 3.3 15.1 - - - +
171H ILE* 4.1 11.4 - - + +
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Residues in contact with LEU 168 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103H LEU* 6.2 0.4 - - + -
144H LEU* 4.5 5.8 - - + -
146H ILE* 3.8 21.1 - - + -
164H MET* 3.0 50.7 + - + +
165H ASN 3.7 4.3 - - - +
166H VAL 3.2 0.2 - - - -
167H ILE* 1.3 77.3 - - + +
169H TRP* 1.3 54.8 + - - +
170H PRO* 3.4 0.2 - - - -
171H ILE* 3.0 11.7 + - + +
172H GLN* 2.8 54.4 + - - +
186H PRO* 4.1 9.6 - - + -
188H LEU* 4.4 3.1 - - + -
268H GLN* 4.0 12.6 - - + +
269H ILE* 3.7 29.6 - - + -
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Residues in contact with TRP 169 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161F HIS 4.1 20.3 + - - -
163F ASP 5.2 1.6 + - - -
166F VAL* 3.8 20.6 - - + +
167F ILE* 4.8 13.3 - - + +
165H ASN 3.2 12.9 + - - +
166H VAL 3.6 7.6 - - - +
168H LEU* 1.3 72.1 - - - +
170H PRO* 1.3 77.0 - - + +
173H SER* 3.1 47.4 + - - -
174H GLY 3.4 1.1 + - - +
222H PHE* 3.6 18.4 - + + -
223H ALA 5.8 0.2 - - - -
254H SER* 3.1 28.7 - - - -
255H VAL* 4.0 13.0 - - + -
256H GLY* 3.3 32.1 - - - -
257H HIS* 4.6 13.2 - + - -
268H GLN* 3.3 31.4 - - - +
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Residues in contact with PRO 170 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105F TRP 4.7 0.4 - - - +
106F PHE* 4.1 28.2 - - + +
166F VAL 4.5 7.9 - - - +
167F ILE* 4.6 12.6 - - + +
170F PRO* 3.9 23.3 - - + -
166H VAL 3.2 13.9 - - - +
167H ILE 3.3 11.7 - - - +
168H LEU 3.4 0.9 - - - -
169H TRP* 1.3 98.7 - - + +
171H ILE* 1.3 60.3 + - + +
174H GLY* 3.0 27.0 - - - +
175H ILE* 3.5 5.9 + - - +
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Residues in contact with ILE 171 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101H PHE* 5.3 3.6 - - + -
103H LEU* 5.5 3.4 - - + -
106H PHE 4.9 0.9 - - - +
107H GLY* 4.3 22.9 - - - -
108H VAL* 4.4 24.2 - - + +
116H PHE* 5.3 4.3 - - + -
144H LEU* 3.7 33.9 - - + -
146H ILE* 5.7 0.9 - - + -
167H ILE* 4.1 18.6 - - + +
168H LEU* 3.0 10.4 + - + +
170H PRO* 1.3 82.1 - - + +
172H GLN* 1.3 62.4 + - - +
175H ILE* 3.0 38.9 + - + +
176H LEU* 3.2 11.3 + - + +
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Residues in contact with GLN 172 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144H LEU* 3.6 32.4 - - + +
168H LEU* 2.8 28.3 + - + +
171H ILE* 1.3 73.9 - - - +
173H SER* 1.3 57.8 + - - +
176H LEU* 3.3 12.9 - - + +
177H HIS* 3.0 26.0 + - - +
183H VAL* 3.7 21.7 - - + +
184H LEU 4.1 2.6 + - - -
186H PRO* 3.7 30.7 - - - +
220H LEU* 3.1 9.8 - - - +
222H PHE* 3.7 8.9 - - + -
268H GLN* 3.0 40.2 + - - +
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Residues in contact with SER 173 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161F HIS 5.2 1.0 + - - -
132H TYR* 3.6 20.5 + - - -
169H TRP* 3.1 43.5 + - - -
172H GLN* 1.3 77.1 - - - +
174H GLY* 1.3 63.4 + - - +
175H ILE 3.5 0.2 + - - -
177H HIS* 3.4 4.4 + - - +
178H PHE 3.1 22.9 + - - -
222H PHE* 3.1 29.7 - - - -
268H GLN* 4.6 0.2 - - - +
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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