Contacts of the helix formed by residues 160 - 179 (chain M) in PDB entry 4UJ3
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 ASN 160 (chain M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151M ILE* 3.2 28.8 - - + +
152M GLU* 3.0 24.0 + - - +
153M THR* 3.6 2.4 - - + +
158M SER 3.2 2.0 + - - -
159M THR* 1.3 78.9 - - - +
161M VAL* 1.3 54.3 + - - +
162M GLU* 3.3 3.1 - - - +
163M ALA* 3.7 10.1 - - - +
164M ALA* 2.7 35.9 + - - +
369Q SER 4.4 0.7 - - - +
370Q ALA* 3.9 2.4 - - - -
371Q VAL* 2.8 38.3 + - - +
372Q GLU* 3.5 22.2 + - - -
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Residues in contact with VAL 161 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27M LEU* 4.0 14.6 - - + +
30M ARG* 3.5 29.4 - - + -
31M PHE* 4.1 19.1 - - + +
153M THR* 4.3 6.1 - - - -
154M SER 3.5 26.7 - - - +
155M ALA* 3.9 14.6 - - - -
158M SER* 3.2 12.5 + - - +
159M THR 2.8 7.2 + - - +
160M ASN* 1.3 79.0 - - - +
162M GLU* 1.3 65.0 + - - +
164M ALA* 3.6 2.1 - - - +
165M PHE* 3.1 36.0 + - + -
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Residues in contact with GLU 162 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31M PHE* 3.8 13.0 - - - -
51M ARG* 2.8 46.9 + - - -
53M ILE* 5.1 0.2 - - - +
158M SER 4.4 3.0 + - - +
160M ASN* 3.3 0.9 - - - -
161M VAL* 1.3 80.9 - - - +
163M ALA* 1.3 62.0 + - - +
164M ALA 3.3 0.3 + - - -
165M PHE* 3.3 4.9 + - - +
166M GLN* 3.0 40.9 + - + +
368Q ALA 3.9 15.9 - - - +
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Residues in contact with ALA 163 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151M ILE* 4.2 4.5 - - + -
160M ASN* 3.4 15.7 + - - +
161M VAL 3.4 0.4 - - - -
162M GLU* 1.3 80.2 - - - +
164M ALA* 1.3 54.7 - - - +
166M GLN* 3.7 0.5 - - - +
167M THR* 2.7 39.9 + - - +
368Q ALA* 4.2 13.4 + - - -
369Q SER* 3.3 35.9 - - - +
370Q ALA* 3.5 11.7 - - + +
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Residues in contact with ALA 164 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27M LEU* 6.2 0.9 - - + -
88M LEU* 5.3 2.2 - - + -
120M MET* 3.1 39.1 - - + +
122M VAL* 5.0 2.0 - - + -
151M ILE* 3.8 16.4 - - + +
153M THR* 3.9 9.2 - - + -
160M ASN 2.7 22.8 + - - +
161M VAL* 3.6 6.1 - - - +
163M ALA* 1.3 75.0 - - - +
165M PHE* 1.3 66.8 + - + +
167M THR* 3.4 1.1 + - - -
168M ILE* 3.3 15.8 + - - +
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Residues in contact with PHE 165 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14M VAL* 5.4 1.3 - - + -
16M LEU* 4.6 6.5 - - + -
27M LEU* 3.8 24.9 - - + -
28M LEU* 5.0 0.4 - - - -
31M PHE* 3.3 65.1 - + + -
64M ILE* 3.9 34.3 - - + -
88M LEU* 3.2 32.5 - - + -
161M VAL* 3.1 27.5 + - + -
162M GLU 3.3 2.5 + - - +
164M ALA* 1.3 78.4 - - + +
166M GLN* 1.3 67.1 + - - +
168M ILE* 3.4 7.0 - - + +
169M LEU* 3.0 35.9 + - + +
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Residues in contact with GLN 166 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31M PHE* 5.5 0.9 - - + -
51M ARG* 5.8 0.6 - - - +
53M ILE* 3.9 42.3 - - + +
54M GLN 4.1 13.8 + - - +
55M VAL* 4.4 3.6 - - - +
162M GLU* 3.0 36.2 + - + +
163M ALA 3.7 0.7 - - - +
165M PHE* 1.3 77.8 - - + +
167M THR* 1.3 58.9 + - - +
169M LEU* 3.8 1.2 - - - +
170M THR* 3.0 36.1 + - + +
368Q ALA* 3.7 38.5 + - + +
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Residues in contact with THR 167 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120M MET* 4.4 13.7 - - - -
149M SER* 4.8 3.6 - - - -
151M ILE* 5.7 1.6 - - - +
163M ALA* 2.7 28.0 + - - +
164M ALA* 3.6 4.5 - - - -
165M PHE 3.2 0.4 - - - -
166M GLN* 1.3 74.5 - - - +
168M ILE* 1.3 66.6 + - - +
170M THR* 2.7 23.4 + - - +
171M GLU* 3.1 27.2 + - - +
368Q ALA* 4.7 7.2 - - - +
370Q ALA* 5.6 4.2 + - - +
398Q SER* 4.5 14.1 - - - +
399Q ASN* 5.2 10.0 + - - +
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Residues in contact with ILE 168 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14M VAL* 4.6 9.0 - - + -
86M GLY* 4.3 3.6 - - - -
87M ALA 3.5 40.2 - - - +
88M LEU* 3.7 21.1 - - + -
118M VAL* 3.5 23.8 - - + +
120M MET* 3.9 16.6 - - + +
149M SER* 5.2 0.4 - - - +
164M ALA 3.3 10.8 + - - +
165M PHE* 3.4 18.2 - - + +
167M THR* 1.3 81.0 - - - +
169M LEU* 1.3 72.3 + - + +
171M GLU* 3.5 9.0 + - - +
172M ILE* 3.2 26.2 + - + +
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Residues in contact with LEU 169 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12M PHE* 4.5 15.3 - - + -
14M VAL* 4.2 22.9 - - + -
31M PHE* 4.6 4.9 - - + -
53M ILE* 3.3 34.1 - - + -
55M VAL* 4.9 2.5 - - + -
60M ILE* 4.4 16.9 - - + +
62M ALA* 3.8 31.4 - - + -
64M ILE* 5.8 0.4 - - + -
165M PHE* 3.0 32.2 + - + +
166M GLN 3.8 3.8 - - - +
168M ILE* 1.3 82.7 - - + +
170M THR* 1.3 59.8 + - - +
172M ILE* 3.3 7.3 + - + +
173M TYR* 3.0 26.3 + - - +
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Residues in contact with THR 170 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55M VAL* 3.3 41.3 - - + -
166M GLN* 3.0 24.6 + - - +
167M THR* 2.7 21.3 + - - -
169M LEU* 1.3 72.8 - - - +
171M GLU* 1.3 63.2 + - - +
173M TYR* 3.3 2.8 + - - +
174M ARG* 3.0 46.3 + - - +
398Q SER* 4.8 5.4 + - - -
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Residues in contact with GLU 171 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118M VAL* 3.5 23.6 - - + +
119M ILE 5.5 0.2 - - - +
149M SER* 3.4 31.4 + - - -
167M THR* 3.1 19.4 + - - +
168M ILE* 3.9 7.4 - - - +
169M LEU 3.3 0.2 - - - -
170M THR* 1.3 77.4 + - - +
172M ILE* 1.3 60.2 + - - +
174M ARG* 3.5 7.1 + - - +
175M ILE* 3.1 31.2 + - + +
398Q SER* 3.5 31.3 - - - +
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Residues in contact with ILE 172 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12M PHE* 3.4 28.0 - - + -
14M VAL* 4.3 13.2 - - + -
85M VAL* 3.6 26.2 - - + +
86M GLY* 3.5 30.7 - - - -
118M VAL* 3.3 24.7 - - + -
168M ILE* 3.2 19.3 + - + +
169M LEU* 3.6 11.7 - - + +
170M THR 3.2 0.2 - - - -
171M GLU* 1.3 73.6 - - - +
173M TYR* 1.3 66.6 + - - +
175M ILE* 3.4 4.0 + - - +
176M VAL* 3.1 27.2 + - + +
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Residues in contact with TYR 173 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10M TYR* 3.8 36.3 + + - -
12M PHE* 4.0 11.8 - + + -
55M VAL* 3.3 29.8 - - + -
56M ASP* 3.1 39.3 + - + -
58M LYS* 3.1 28.7 - - + +
60M ILE* 4.9 6.7 - - + -
169M LEU 3.0 13.6 + - - +
170M THR* 3.3 11.4 - - - +
172M ILE* 1.3 76.9 - - - +
174M ARG* 1.3 65.9 + - - +
176M VAL* 3.0 2.9 + - - -
177M SER* 2.9 52.6 + - - -
180M GLN* 5.1 2.8 + - - -
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Residues in contact with ARG 174 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55M VAL* 5.6 1.4 - - - +
56M ASP* 4.6 22.2 + - - +
170M THR* 3.0 34.4 + - - +
171M GLU* 3.7 8.9 - - - +
173M TYR* 1.3 84.2 - - - +
175M ILE* 1.3 64.3 + - + +
177M SER* 3.5 8.0 + - - -
178M GLN* 3.3 22.5 + - - +
398Q SER* 6.0 0.6 + - - -
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Residues in contact with ILE 175 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116M ASN* 5.2 13.7 - - + +
118M VAL* 4.6 13.5 - - + -
171M GLU* 3.1 17.4 + - + +
172M ILE* 3.7 8.3 - - - +
173M TYR 3.2 0.4 - - - -
174M ARG* 1.3 79.2 - - + +
176M VAL* 1.3 64.0 + - + +
178M GLN* 3.5 16.8 + - + +
179M LYS* 3.7 6.4 + - - +
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Residues in contact with VAL 176 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10M TYR* 4.0 25.4 - - + -
12M PHE* 3.7 24.5 - - + -
85M VAL* 6.2 2.9 - - + -
172M ILE* 3.1 21.1 + - + +
173M TYR 3.0 5.0 + - - +
175M ILE* 1.3 78.8 - - + +
177M SER* 1.3 64.3 + - - +
179M LYS* 3.1 23.4 - - + +
180M GLN* 3.8 5.7 + - - +
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Residues in contact with SER 177 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10M TYR* 5.2 0.4 + - - -
173M TYR* 2.9 46.2 + - - -
174M ARG* 3.8 8.2 - - - -
175M ILE 3.4 0.2 - - - -
176M VAL* 1.3 72.9 - - - +
178M GLN* 1.3 56.1 + - - +
179M LYS 3.0 2.2 - - - -
180M GLN* 2.8 53.4 + - - +
181M MET 4.3 0.3 + - - -
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Residues in contact with GLN 178 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174M ARG 3.3 11.7 + - - +
175M ILE* 3.7 13.2 - - + +
176M VAL 3.3 0.4 - - - -
177M SER* 1.3 77.6 - - - +
179M LYS* 1.3 59.0 + - - +
180M GLN 3.1 1.8 + - - -
181M MET* 3.4 18.9 + - - +
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Residues in contact with LYS 179 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175M ILE 3.7 6.4 + - - +
176M VAL* 3.1 22.0 + - + +
177M SER 3.0 0.2 - - - -
178M GLN* 1.3 75.0 - - - +
180M GLN* 1.3 57.5 + - - +
181M MET 3.0 16.5 + - - +
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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) + - + + + + + -
------------------------------------------------------------
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