Contacts of the helix formed by residues 164 - 178 (chain J) in PDB entry 6AHU
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 THR 164 (chain J).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162J ASP* 3.7 15.5 + - + +
163J SER* 1.3 81.5 - - - +
165J MET* 1.3 66.0 + - - +
166J ARG 3.2 1.1 - - - -
167J ARG* 3.3 27.1 + - - +
168J TYR* 3.2 27.6 - - - -
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Residues in contact with MET 165 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129J VAL 5.4 2.0 - - - +
130J THR* 3.9 32.8 - - + -
131J GLU* 5.9 3.8 - - + +
157J SER* 3.9 20.4 - - - +
158J PRO* 3.6 15.4 - - + +
160J ILE* 6.0 2.5 - - + -
161J LYS* 5.2 10.8 - - - -
162J ASP* 3.7 30.3 - - + +
163J SER 3.2 1.0 - - - -
164J THR* 1.3 77.6 + - - +
166J ARG* 1.3 62.2 + - - +
167J ARG 3.2 1.7 + - - -
168J TYR* 3.5 11.9 + - + +
169J THR* 3.3 29.4 + - + +
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Residues in contact with ARG 166 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43E THR* 3.7 24.1 + - - +
50H ASP* 3.6 23.8 + - - +
51H LEU* 3.4 19.8 - - + +
91H LEU* 2.9 56.4 + - + +
92H LEU* 4.6 5.7 + - - +
93H GLY* 5.1 3.8 - - - +
158J PRO* 3.7 22.5 + - + +
159J ALA* 4.4 9.9 - - - +
163J SER* 3.5 33.3 - - - +
164J THR 3.2 0.8 - - - -
165J MET* 1.3 77.5 - - - +
167J ARG* 1.3 60.4 + - - +
169J THR* 3.1 15.0 + - - -
170J ILE* 3.4 14.9 - - - +
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Residues in contact with ARG 167 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34E ARG 5.3 3.6 + - - -
38E ALA* 3.4 27.9 - - - +
43E THR* 4.0 33.2 - - + +
46E ALA* 4.0 20.1 + - + +
47E ALA* 3.3 16.4 - - + +
164J THR* 3.3 25.0 + - - +
165J MET 3.2 0.6 - - - -
166J ARG* 1.3 78.4 - - - +
168J TYR* 1.3 68.4 + - + +
170J ILE* 3.3 5.4 - - - +
171J SER* 3.0 31.4 + - - -
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Residues in contact with TYR 168 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129J VAL* 3.5 47.5 + - + +
130J THR* 5.9 0.2 - - - -
131J GLU* 5.0 7.2 - - - -
132J LYS* 3.3 52.0 - - + +
133J LEU 5.1 0.7 - - - -
164J THR* 3.2 34.3 - - - -
165J MET* 3.5 9.9 + - + +
166J ARG 3.4 0.2 - - - -
167J ARG* 1.3 83.6 - - + +
169J THR* 1.3 60.6 + - - +
171J SER* 3.4 15.6 + - - -
172J SER* 3.2 17.0 + - - -
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Residues in contact with THR 169 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129J VAL 5.1 7.0 - - - +
154J LEU* 5.5 1.6 - - - +
155J VAL 5.2 3.6 - - - +
156J TYR* 4.9 9.9 - - - -
157J SER 4.9 7.4 - - - +
158J PRO* 4.3 23.1 - - + +
165J MET* 3.3 17.8 + - + +
166J ARG* 3.1 15.4 + - - -
168J TYR* 1.3 79.4 - - - +
170J ILE* 1.3 65.3 + - - +
171J SER 3.3 0.2 - - - -
172J SER* 3.6 4.9 + - - -
173J ALA* 3.3 25.3 + - - +
210J PHE* 4.0 14.7 - - - -
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Residues in contact with ILE 170 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43E THR 3.7 20.2 - - - +
44E PHE* 3.6 43.3 - - + +
47E ALA* 3.7 8.7 - - + -
48E ALA 4.9 0.4 - - - +
166J ARG 3.4 13.5 - - - +
167J ARG 3.3 14.1 - - - +
169J THR* 1.3 80.2 + - - +
171J SER* 1.3 63.9 + - - +
174J LEU* 3.3 34.6 + - + +
209J LEU* 3.9 17.7 - - + +
210J PHE* 3.6 30.1 - - + -
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Residues in contact with SER 171 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47E ALA* 3.9 17.5 - - - -
51E ILE* 3.8 23.8 - - - +
129J VAL* 5.5 1.0 - - - +
167J ARG 3.0 18.0 + - - -
168J TYR* 3.4 19.1 + - - +
170J ILE* 1.3 77.0 - - - +
172J SER* 1.3 71.1 + - - +
174J LEU* 4.0 2.9 - - - +
175J ASN* 2.8 31.3 + - - -
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Residues in contact with SER 172 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127J ILE* 4.9 7.6 + - - +
128J THR* 5.5 0.2 - - - -
129J VAL* 3.7 31.0 + - - +
137J PHE* 3.2 34.2 - - - -
154J LEU* 4.7 10.7 - - - +
168J TYR 3.2 13.6 + - - -
169J THR* 3.6 6.4 + - - -
171J SER* 1.3 79.2 + - - +
173J ALA* 1.3 65.5 + - - +
175J ASN* 3.7 8.7 + - - +
176J LEU* 3.4 4.5 + - - +
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Residues in contact with ALA 173 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154J LEU* 3.8 28.0 - - + -
169J THR 3.3 16.7 + - - +
170J ILE 4.3 1.3 - - - +
171J SER 3.3 1.0 - - - -
172J SER* 1.3 80.8 + - - +
174J LEU* 1.3 58.8 + - - +
176J LEU* 3.0 8.0 + - - +
177J MET* 3.0 31.9 + - + +
210J PHE* 3.6 31.2 - - + -
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Residues in contact with LEU 174 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44E PHE* 4.4 5.6 - - + -
48E ALA* 3.7 21.1 - - + -
51E ILE* 5.7 6.3 - - + -
73E PHE* 3.7 37.0 - - + -
170J ILE* 3.3 36.1 + - + +
171J SER* 4.2 2.9 - - - +
173J ALA* 1.3 75.1 - - + +
175J ASN* 1.3 63.5 + - - +
176J LEU 3.2 0.2 - - - -
177J MET* 3.9 6.9 - - + +
178J GLN* 3.4 34.0 + - + +
209J LEU 4.7 2.5 - - - +
210J PHE* 3.4 30.7 - - - +
3L THR* 4.9 11.9 - - + -
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Residues in contact with ASN 175 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51E ILE* 3.4 42.7 - - - +
70E ARG* 5.2 2.1 + - - -
135J PHE 5.4 5.9 + - - +
137J PHE* 3.6 15.3 - - + -
171J SER 2.8 24.6 + - - +
172J SER* 3.8 11.0 - - - +
173J ALA 3.2 0.2 - - - -
174J LEU* 1.3 78.1 - - - +
176J LEU* 1.3 59.6 + - - +
178J GLN* 4.0 5.2 + - - +
179J ILE* 3.3 31.0 + - + +
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Residues in contact with LEU 176 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127J ILE* 4.6 21.3 - - + -
137J PHE* 3.6 27.3 - - + -
142J ILE* 4.5 19.1 - - + -
152J PHE* 4.9 7.2 - - + -
154J LEU* 4.9 12.3 - - + -
172J SER 3.4 4.7 + - - +
173J ALA* 3.0 10.3 + - - +
175J ASN* 1.3 79.0 - - - +
177J MET* 1.3 76.7 + - + +
179J ILE* 3.1 2.6 + - + -
180J CYS* 2.6 59.1 + - + +
185J VAL* 3.9 22.0 - - + -
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Residues in contact with MET 177 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154J LEU* 4.9 5.4 - - + -
173J ALA* 3.0 18.5 + - + +
174J LEU* 3.7 8.3 + - + +
175J ASN 3.5 0.4 - - - -
176J LEU* 1.3 105.2 - - + +
178J GLN* 1.3 60.1 + - + +
179J ILE 3.5 0.3 + - - -
180J CYS* 4.7 1.1 - - + +
181J LYS* 3.8 19.9 + - - +
182J GLY* 4.7 6.7 - - - -
185J VAL* 4.0 25.1 - - + -
210J PHE* 3.4 28.5 - - + +
212J LEU* 3.7 41.1 - - + +
3L THR* 6.2 3.8 - - + -
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Residues in contact with GLN 178 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4E PHE* 3.8 31.7 - - + -
51E ILE* 4.8 8.9 - - - +
70E ARG* 4.5 18.6 + - - +
72E GLU* 3.4 34.5 + - + +
73E PHE* 4.1 24.0 - - - -
174J LEU* 3.4 19.9 + - + +
175J ASN* 4.0 6.4 + - - +
176J LEU 3.3 0.6 - - - -
177J MET* 1.3 78.5 - - + +
179J ILE* 1.3 60.6 + - - +
181J LYS* 4.9 1.1 - - - -
3L THR* 5.7 4.9 - - + +
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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