Contacts of the helix formed by residues 164 - 180 (chain B) in PDB entry 3U1K
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 GLU 164 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109B ALA* 5.3 9.0 - - - +
126B LYS* 3.2 24.7 + - - -
162B VAL 3.6 5.2 + - - +
163B ASN* 1.3 70.5 - - - +
165B PRO* 1.3 80.6 - - - +
166B ASP* 3.2 33.1 + - - +
167B VAL* 4.2 5.1 + - + +
168B LEU* 3.7 17.4 - - - +
192B ARG* 3.9 9.6 - - - +
204B PRO 5.0 7.6 + - - +
206B ARG* 5.4 12.0 + - + +
209B MET* 3.9 28.6 - - - +
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Residues in contact with PRO 165 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78B THR* 3.9 9.4 - - + -
80B VAL* 3.6 23.9 - - + +
102B TYR* 3.2 23.6 - - - +
104B GLN* 5.8 1.3 - - - +
109B ALA* 6.4 0.9 - - + -
126B LYS* 4.7 3.6 - - - +
156B LEU* 4.1 17.0 - - + -
159B VAL* 4.3 13.7 - - + -
163B ASN 3.6 7.2 - - - +
164B GLU* 1.3 98.7 - - - +
166B ASP* 1.3 63.4 + - - +
167B VAL 3.4 0.2 - - - -
168B LEU* 3.0 10.7 + - + +
169B ALA* 2.9 22.7 + - - +
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Residues in contact with ASP 166 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102B TYR* 4.1 7.0 - - - +
126B LYS* 3.8 13.1 - - - -
130B THR* 3.6 32.2 + - + +
133B ILE* 5.7 3.8 - - + -
164B GLU* 3.2 20.1 + - - +
165B PRO* 1.3 78.5 - - - +
167B VAL* 1.3 78.6 + - - +
169B ALA* 3.1 5.5 + - - +
170B ILE* 3.1 25.7 + - + +
192B ARG* 2.7 42.5 + - - -
209B MET* 5.6 0.2 - - - +
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Residues in contact with VAL 167 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56B LEU* 6.3 0.2 - - + -
164B GLU* 4.2 3.3 + - + +
165B PRO 3.4 0.6 - - - -
166B ASP* 1.3 92.5 + - - +
168B LEU* 1.3 66.4 + - + +
170B ILE* 3.3 10.0 + - + +
171B ASN* 2.9 32.0 + - - +
190B ALA* 3.3 28.5 - - + +
191B VAL* 3.8 12.3 - - - -
192B ARG* 3.6 38.4 - - + +
203B ASN* 3.8 15.9 - - - +
217B VAL* 4.5 12.1 - - + -
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Residues in contact with LEU 168 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56B LEU* 4.1 25.6 - - + -
73B VAL* 3.7 33.1 - - + +
75B SER* 4.1 17.0 - - - +
78B THR* 3.8 41.3 - - + +
80B VAL* 3.9 12.7 - - + +
163B ASN 5.0 1.3 - - - +
164B GLU 3.7 18.6 - - - +
165B PRO* 3.0 8.0 + - + +
167B VAL* 1.3 83.7 - - + +
169B ALA* 1.3 58.2 + - - +
171B ASN* 3.3 4.1 + - - +
172B GLY* 2.8 25.6 + - - -
203B ASN* 5.3 3.8 - - - +
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Residues in contact with ALA 169 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80B VAL* 3.9 18.1 - - + +
82B VAL* 3.7 5.5 - - - +
102B TYR* 3.7 34.5 - - + -
134B ILE* 3.8 12.0 - - + +
154B CYS* 4.0 6.0 - - - -
165B PRO 2.9 6.9 + - - +
166B ASP 3.1 9.2 + - - +
168B LEU* 1.3 74.1 - - - +
170B ILE* 1.3 65.8 + - - +
172B GLY* 3.1 0.3 + - - -
173B ALA* 2.8 24.8 + - - +
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Residues in contact with ILE 170 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133B ILE* 4.1 20.2 - - + -
134B ILE* 3.8 26.9 - - + +
137B SER* 3.7 28.5 - - - +
138B ILE* 5.0 2.0 - - + +
166B ASP* 3.1 16.0 + - - +
167B VAL* 3.3 12.5 + - + +
169B ALA* 1.3 76.2 - - - +
171B ASN* 1.3 63.1 + - - +
173B ALA* 3.4 4.2 + - - +
174B SER* 3.2 19.1 + - - -
188B VAL* 4.7 7.4 - - + -
190B ALA* 3.6 24.0 - - + -
217B VAL* 3.8 28.9 - - + -
228B MET* 4.8 0.2 - - + -
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Residues in contact with ASN 171 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56B LEU* 4.2 11.1 - - + +
58B ILE* 5.5 1.6 - - + -
73B VAL* 4.1 15.5 - - + -
167B VAL* 2.9 26.7 + - - +
168B LEU* 3.7 7.4 - - - +
170B ILE* 1.3 76.5 - - - +
172B GLY* 1.3 57.9 + - - +
174B SER* 3.0 8.9 + - - -
175B VAL* 2.8 35.1 + - + +
188B VAL 4.1 0.5 - - - +
189B GLY* 3.4 3.8 - - - -
190B ALA* 2.9 43.2 + - - +
255B ILE* 3.4 27.3 - - + +
259B ILE* 5.5 0.9 - - + -
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Residues in contact with GLY 172 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B ALA* 4.0 5.1 - - - +
73B VAL* 3.6 18.8 - - - +
80B VAL 5.6 0.2 - - - -
82B VAL* 3.5 19.8 - - - +
168B LEU 2.8 16.3 + - - -
169B ALA 3.1 4.0 + - - -
171B ASN* 1.3 70.2 - - - +
173B ALA* 1.3 58.6 + - - +
175B VAL* 3.8 2.7 - - - +
176B ALA* 2.9 32.2 + - - +
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Residues in contact with ALA 173 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82B VAL* 3.6 12.5 - - + +
134B ILE* 3.8 24.5 - - + -
138B ILE* 4.1 13.9 - - + -
152B VAL* 3.9 16.4 - - + -
154B CYS* 5.9 0.2 - - - -
169B ALA 2.8 15.5 + - - +
170B ILE 3.6 8.7 - - - +
172B GLY* 1.3 71.3 - - - +
174B SER* 1.3 64.9 + - - +
176B ALA* 3.8 1.4 - - - +
177B LEU* 3.0 32.1 + - + +
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Residues in contact with SER 174 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138B ILE* 4.8 1.3 - - - +
170B ILE 3.2 9.4 + - - -
171B ASN* 3.0 10.2 + - - -
173B ALA* 1.3 79.6 - - - +
175B VAL* 1.3 54.8 + - - +
178B SER* 2.6 37.1 + - - -
184B TRP* 3.4 20.4 - - - -
187B PRO* 3.7 6.2 - - - +
188B VAL* 2.7 48.7 + - - -
259B ILE* 3.7 2.6 - - - +
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Residues in contact with VAL 175 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58B ILE* 3.6 35.4 - - + -
59B SER 5.0 0.2 - - - +
71B ALA* 3.5 24.2 - - + -
73B VAL* 4.7 2.0 - - + -
171B ASN 2.8 24.4 + - - +
172B GLY* 4.6 0.2 - - - -
174B SER* 1.3 72.8 - - - +
176B ALA* 1.3 67.2 + - - +
178B SER* 3.1 5.5 + - - -
179B LEU* 2.8 48.6 + - + +
259B ILE* 3.8 27.4 - - + -
262B LEU* 3.9 7.4 - - + -
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Residues in contact with ALA 176 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69B GLY* 3.6 9.9 - - - +
70B SER* 3.8 19.3 - - - +
71B ALA* 3.8 4.6 - - - +
82B VAL* 3.5 26.9 - - + +
83B THR 4.4 0.7 - - - -
84B ALA* 4.3 11.0 - - + +
172B GLY 2.9 18.8 + - - +
173B ALA 3.8 3.4 - - - +
175B VAL* 1.3 78.2 - - - +
177B LEU* 1.3 61.9 + - - +
179B LEU* 3.9 0.9 - - - -
180B SER* 3.0 25.7 + - - -
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Residues in contact with LEU 177 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84B ALA* 4.0 21.5 - - + -
138B ILE* 3.9 22.7 - - + -
142B PHE* 3.8 30.7 - - + -
150B THR* 5.1 2.2 - - + -
152B VAL* 4.7 5.6 - - + -
173B ALA 3.0 20.3 + - - +
176B ALA* 1.3 76.4 - - - +
178B SER* 1.3 60.3 + - - +
180B SER* 2.8 19.5 + - - -
182B ILE* 3.9 21.4 - - + +
184B TRP* 3.7 43.7 - - + +
270B LYS* 2.9 16.3 + - - -
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Residues in contact with SER 178 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174B SER 2.6 25.6 + - - -
175B VAL 3.1 3.6 + - - -
177B LEU* 1.3 78.3 - - - +
179B LEU* 1.3 61.2 + - - +
180B SER 3.7 0.7 - - - +
184B TRP* 3.4 18.4 - - - -
186B GLY 5.1 0.3 - - - -
187B PRO* 3.6 17.0 - - - +
259B ILE* 3.9 6.9 - - - +
263B VAL* 3.7 35.8 - - - +
267B GLY* 4.8 1.9 - - - -
268B VAL 5.4 0.9 + - - +
270B LYS* 3.5 17.2 + - - +
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Residues in contact with LEU 179 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60B SER* 3.5 34.8 - - - +
69B GLY* 5.7 0.4 - - - -
70B SER 4.2 5.8 - - - +
175B VAL* 2.8 38.8 + - + +
176B ALA* 4.0 3.4 - - - +
178B SER* 1.3 69.4 - - - +
180B SER* 1.3 67.0 + - - +
259B ILE* 6.0 0.2 - - + -
262B LEU* 4.0 24.0 - - + +
263B VAL* 4.1 17.0 - - + +
266B THR* 3.7 28.6 - - + +
267B GLY* 3.7 5.3 - - - -
268B VAL* 3.1 26.3 + - - +
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Residues in contact with SER 180 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68B ASP 3.2 31.6 - - - -
69B GLY* 3.7 2.9 - - - -
176B ALA 3.0 15.0 + - - -
177B LEU* 2.8 18.5 + - - -
178B SER 3.3 0.4 - - - +
179B LEU* 1.3 82.4 - - - +
181B ASP* 1.3 60.0 + - - +
182B ILE* 3.1 29.5 + - - +
268B VAL* 3.5 8.1 - - - +
270B LYS* 2.9 23.2 + - - +
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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
------------------------------------------------------------
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