Contacts of the helix formed by residues 160 - 180 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151D ILE* 3.5 23.5 - - + +
152D GLU* 3.1 28.3 + - - +
153D THR* 3.7 3.1 - - + -
158D SER 3.2 2.8 + - - -
159D THR* 1.3 81.0 - - - +
161D VAL* 1.3 54.3 + - - +
162D GLU* 3.3 2.9 - - - +
163D ALA* 3.7 15.9 - - - +
164D ALA* 2.7 35.9 + - - +
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Residues in contact with VAL 161 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27D LEU* 4.0 25.4 - - + +
30D ARG* 3.6 30.5 - - + -
31D PHE* 4.3 4.9 - - + +
153D THR* 4.0 13.0 - - - -
154D SER 3.4 31.9 - - - +
155D ALA* 3.7 10.3 - - - +
158D SER 3.4 9.3 + - - +
159D THR 2.8 13.2 + - - +
160D ASN* 1.3 75.8 - - - +
162D GLU* 1.3 64.7 + - - +
164D ALA* 3.3 7.8 + - - +
165D PHE* 3.3 23.8 + - + -
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Residues in contact with GLU 162 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30D ARG 5.5 2.4 - - - +
31D PHE* 3.6 14.3 - - - -
51D ARG* 2.5 48.1 + - - -
158D SER 4.5 3.2 + - - +
160D ASN 3.3 0.2 - - - -
161D VAL* 1.3 80.3 - - - +
163D ALA* 1.3 62.0 + - - +
164D ALA 3.2 0.3 + - - -
165D PHE* 3.2 4.3 + - - +
166D GLN* 2.9 44.7 + - + +
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Residues in contact with ALA 163 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151D ILE* 4.2 9.2 - - + -
160D ASN* 3.3 24.2 + - - +
162D GLU* 1.3 79.6 - - - +
164D ALA* 1.3 57.2 + - - +
166D GLN* 3.7 7.2 - - - +
167D THR* 2.8 38.4 + - - +
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Residues in contact with ALA 164 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27D LEU* 6.2 1.1 - - + -
88D LEU* 5.7 1.3 - - + -
120D MET* 3.0 40.2 - - + +
122D VAL* 5.1 2.2 - - + -
151D ILE* 3.7 20.4 - - + +
153D THR* 3.9 9.0 - - + -
160D ASN 2.7 21.3 + - - +
161D VAL* 3.5 6.1 - - - +
162D GLU 3.2 0.2 - - - -
163D ALA* 1.3 74.9 - - - +
165D PHE* 1.3 64.9 + - + +
167D THR* 3.8 1.1 - - - -
168D ILE* 3.2 14.7 + - - +
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Residues in contact with PHE 165 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16D LEU* 4.8 2.0 - - + -
27D LEU* 3.6 30.3 - - + -
28D LEU* 4.8 0.7 - - - -
31D PHE* 3.3 55.6 - + + -
64D ILE* 3.7 42.6 - - + -
88D LEU* 3.3 31.2 - - + -
161D VAL* 3.3 25.7 + - + -
162D GLU 3.2 3.0 + - - +
164D ALA* 1.3 79.1 - - + +
166D GLN* 1.3 66.5 + - - +
168D ILE* 3.4 7.8 - - + +
169D LEU* 2.9 35.4 + - + +
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Residues in contact with GLN 166 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31D PHE* 5.4 2.2 - - + -
51D ARG* 4.9 2.6 - - - +
53D ILE* 4.6 25.5 - - + +
54D GLN 4.9 8.3 - - - +
55D VAL* 5.2 0.3 - - - +
162D GLU* 2.9 46.3 + - + +
163D ALA* 3.7 7.2 - - - +
165D PHE* 1.3 77.0 - - + +
167D THR* 1.3 62.1 + - - +
169D LEU* 4.0 6.1 - - - +
170D THR* 3.1 36.7 + - + +
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Residues in contact with THR 167 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120D MET* 4.6 10.1 - - - -
149D SER* 5.3 2.7 - - - -
151D ILE* 5.5 2.8 - - - +
163D ALA* 2.8 25.3 + - - +
164D ALA* 3.8 5.2 - - - -
165D PHE 3.1 0.2 - - - -
166D GLN* 1.3 75.3 - - - +
168D ILE* 1.3 67.2 + - - +
170D THR* 3.0 21.6 + - - +
171D GLU* 3.0 41.5 + - + +
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Residues in contact with ILE 168 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14D VAL* 4.4 10.5 - - + -
86D GLY* 4.5 1.8 - - - -
87D ALA 3.6 29.4 - - - +
88D LEU* 3.5 32.5 - - + -
118D VAL* 3.6 23.3 - - + +
120D MET* 3.8 15.9 - - + +
164D ALA 3.2 13.4 + - - +
165D PHE* 3.4 16.8 - - + +
167D THR* 1.3 78.6 - - - +
169D LEU* 1.3 69.0 + - + +
171D GLU* 3.6 10.8 + - - +
172D ILE* 3.1 31.7 + - + +
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Residues in contact with LEU 169 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12D PHE* 4.1 24.8 - - + -
14D VAL* 4.1 23.8 - - + -
31D PHE* 4.4 13.0 - - + -
53D ILE* 3.9 31.6 - - + -
55D VAL* 5.3 1.6 - - - -
60D ILE* 4.7 5.3 - - + +
62D ALA* 3.7 33.2 - - + -
64D ILE* 5.5 0.4 - - + -
165D PHE* 2.9 30.8 + - + +
166D GLN* 4.0 4.9 - - - +
168D ILE* 1.3 79.0 - - + +
170D THR* 1.3 59.1 + - - +
172D ILE* 3.1 6.3 + - + +
173D TYR* 2.9 25.8 + - - +
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Residues in contact with THR 170 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55D VAL* 3.4 35.2 - - + -
166D GLN* 3.1 19.6 + - + +
167D THR* 3.0 16.4 + - - +
169D LEU* 1.3 73.4 - - - +
171D GLU* 1.3 63.4 + - - +
173D TYR* 3.1 10.8 + - - +
174D ARG* 2.8 30.5 + - - +
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Residues in contact with GLU 171 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118D VAL* 4.0 16.9 - - + +
149D SER* 3.5 28.2 + - - -
167D THR* 3.0 37.3 + - + +
168D ILE* 3.8 11.7 - - - +
170D THR* 1.3 81.2 - - - +
172D ILE* 1.3 59.5 + - - +
174D ARG* 3.8 13.7 + - - +
175D ILE* 3.1 33.6 + - + +
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Residues in contact with ILE 172 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12D PHE* 3.7 24.9 - - + -
14D VAL* 4.2 13.2 - - + -
85D VAL* 3.1 51.8 - - + +
86D GLY* 3.5 12.1 - - - -
118D VAL* 3.4 24.0 - - + -
168D ILE* 3.1 20.8 + - + +
169D LEU* 3.1 8.9 + - + +
171D GLU* 1.3 75.2 - - - +
173D TYR* 1.3 65.0 + - - +
175D ILE* 3.4 3.5 + - - +
176D VAL* 3.0 31.3 + - + +
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Residues in contact with TYR 173 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10D TYR* 3.7 27.8 - + - -
12D PHE* 3.8 7.8 - - + -
55D VAL* 4.0 22.7 - - + -
56D ASP* 3.1 36.8 + - + -
58D LYS* 3.6 24.1 + - + +
60D ILE* 3.8 20.4 - - + -
169D LEU 2.9 12.7 + - - +
170D THR* 3.3 13.2 - - - +
172D ILE* 1.3 77.6 - - - +
174D ARG* 1.3 64.5 + - + +
176D VAL* 3.0 7.3 - - - +
177D SER* 2.9 57.5 + - - -
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Residues in contact with ARG 174 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170D THR 2.8 19.4 + - - +
171D GLU* 3.8 13.4 + - - +
172D ILE 3.3 0.2 - - - -
173D TYR* 1.3 80.2 - - + +
175D ILE* 1.3 94.9 + - - +
177D SER* 4.0 2.3 - - - -
178D GLN* 2.9 71.5 + - + +
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Residues in contact with ILE 175 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116D ASN* 5.0 16.4 - - + +
118D VAL* 4.6 13.0 - - + -
171D GLU* 3.1 20.6 + - + +
172D ILE* 4.0 4.7 - - - +
173D TYR 3.3 0.4 - - - -
174D ARG* 1.3 106.8 - - - +
176D VAL* 1.3 65.2 + - + +
178D GLN* 4.2 3.4 - - - +
179D LYS* 3.3 23.0 + - + +
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Residues in contact with VAL 176 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10D TYR* 4.2 16.6 - - + -
12D PHE* 3.8 24.5 - - + -
85D VAL* 5.9 5.8 - - + -
172D ILE* 3.0 24.8 + - + +
173D TYR* 3.0 18.8 - - - +
175D ILE* 1.3 80.8 - - + +
177D SER* 1.3 63.8 + - - +
178D GLN 3.3 0.2 - - - -
179D LYS* 3.6 5.3 + - - +
180D GLN* 3.3 20.3 + - - +
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Residues in contact with SER 177 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10D TYR* 4.0 9.3 + - - -
173D TYR* 2.9 58.6 + - - -
174D ARG* 4.0 3.6 - - - -
176D VAL* 1.3 77.2 - - - +
178D GLN* 1.3 62.1 + - - +
180D GLN* 3.0 36.3 + - - +
181D MET* 3.1 7.8 + - - +
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Residues in contact with GLN 178 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174D ARG* 2.9 60.7 + - + +
175D ILE* 4.2 4.3 - - - +
177D SER* 1.3 74.8 - - - +
179D LYS* 1.3 63.8 + - - +
180D GLN 3.1 1.3 - - - -
181D MET* 3.0 25.9 + - + +
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Residues in contact with LYS 179 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175D ILE* 3.3 16.5 + - + +
176D VAL* 3.6 6.5 + - - +
177D SER 3.3 0.2 - - - -
178D GLN* 1.3 77.6 - - - +
180D GLN* 1.3 60.0 + - - +
181D MET 3.5 7.1 + - - +
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Residues in contact with GLN 180 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10D TYR* 4.1 15.5 + - - -
58D LYS* 4.9 7.1 - - - +
176D VAL 3.3 12.1 + - - +
177D SER* 3.0 22.4 + - - +
179D LYS* 1.3 78.0 - - - +
181D MET* 1.3 62.3 + - - +
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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) + - + + + + + -
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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