Contacts of the helix formed by residues 176 - 194 (chain A) in PDB entry 5TWF
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 176 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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167A PHE* 5.4 3.8 - - + -
170A VAL* 4.3 8.9 - - + +
171A MET* 3.1 54.0 - - + +
173A LEU 4.8 2.0 - - - +
174A GLU 3.2 9.4 + - - +
175A GLU* 1.3 77.5 + - - +
177A ALA* 1.3 64.2 + - - +
178A HIS* 3.1 3.8 + - - +
179A LEU* 3.3 13.5 + - - +
180A ASN* 2.6 28.0 + - - +
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Residues in contact with ALA 177 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176A GLU* 1.3 80.3 - - + +
178A HIS* 1.3 53.2 + - - +
179A LEU 3.4 0.2 - - - -
180A ASN* 3.8 9.5 - - - +
181A THR* 2.6 43.4 + - + +
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Residues in contact with HIS 178 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A GLN* 2.9 30.5 + - - -
70A MET* 5.5 4.9 - - + -
71A LEU* 3.7 22.4 - - + +
175A GLU* 2.5 46.0 + - - +
176A GLU 3.1 2.4 - - - +
177A ALA* 1.3 77.6 - - - +
179A LEU* 1.3 56.4 + - - +
181A THR* 2.5 20.8 + - - -
182A SER* 2.9 17.1 + - - -
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Residues in contact with LEU 179 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A LEU* 3.5 34.5 - - + +
159A TYR* 4.5 9.6 - - + -
162A ILE* 3.4 40.2 - - + -
163A TYR* 3.3 42.2 - - + +
167A PHE* 6.0 3.1 - - + -
170A VAL* 4.8 14.6 - - + -
175A GLU* 4.3 4.5 + - - +
176A GLU 3.3 9.8 + - - +
178A HIS* 1.3 80.1 - - - +
180A ASN* 1.3 63.9 + - - +
182A SER* 4.0 0.7 - - - -
183A PHE* 2.8 31.2 + - - +
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Residues in contact with ASN 180 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163A TYR* 2.8 35.8 + - - +
167A PHE* 5.2 10.4 - - - -
176A GLU* 2.6 33.7 + - - +
177A ALA* 3.8 7.0 - - - +
178A HIS 3.3 0.4 - - - -
179A LEU* 1.3 76.9 - - - +
181A THR* 1.3 61.7 + - + +
183A PHE* 3.8 1.1 - - - +
184A LYS* 2.9 31.4 + - - +
207A LEU* 5.2 2.6 - - - +
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Residues in contact with THR 181 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41A LEU* 4.6 3.6 - - - +
177A ALA* 2.6 23.3 + - + +
178A HIS* 2.5 28.2 + - - -
180A ASN* 1.3 76.2 - - + +
182A SER* 1.3 55.0 + - - +
184A LYS* 3.3 8.7 + - + +
185A HIS* 2.9 29.2 + - - +
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Residues in contact with SER 182 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64A PHE* 4.4 5.2 - - - -
67A GLN* 3.8 27.1 - - - +
68A ILE* 4.1 2.9 - - - +
71A LEU* 4.1 15.5 - - - -
159A TYR* 3.0 19.3 + - - -
178A HIS* 2.9 23.2 + - - -
179A LEU 4.1 0.2 - - - -
181A THR* 1.3 76.9 + - - +
183A PHE* 1.3 58.0 + - - +
185A HIS* 3.4 9.7 - - - +
186A PHE* 2.8 23.4 + - - +
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Residues in contact with PHE 183 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156A PHE* 3.7 10.8 - + - -
159A TYR* 3.1 53.8 + + + -
163A TYR* 3.9 20.9 - + + +
179A LEU 2.8 20.8 + - - +
180A ASN 3.8 3.4 - - - +
182A SER* 1.3 74.5 + - - +
184A LYS* 1.3 62.4 + - - +
186A PHE* 3.1 1.2 + - - +
187A ILE* 2.8 62.4 + - + +
204A LEU* 3.5 40.4 - - + -
207A LEU* 4.3 15.3 - - + -
208A ILE* 5.3 4.5 - - + -
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Residues in contact with LYS 184 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39A GLY* 4.1 17.2 + - - -
41A LEU* 3.6 22.0 - - + +
180A ASN 2.9 19.7 + - - +
181A THR* 3.6 7.2 - - + +
183A PHE* 1.3 79.8 - - - +
185A HIS* 1.3 62.5 + - - +
187A ILE* 4.2 3.1 - - - +
188A PHE* 3.0 59.2 + - + -
211A LEU* 4.4 18.4 - - + +
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Residues in contact with HIS 185 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32A ALA* 5.0 8.7 + - + +
33A GLU* 6.0 0.2 - - - -
36A LEU* 3.7 40.9 - - + +
41A LEU* 3.6 13.7 - - + +
44A ALA 5.8 0.2 + - - -
45A VAL* 3.7 23.6 - - + +
60A ASN* 4.2 15.5 + - + -
63A ASP* 5.1 11.4 + - + -
64A PHE* 3.4 26.3 - + - -
181A THR 2.9 14.1 + - - +
182A SER* 3.4 12.6 + - - +
184A LYS* 1.3 77.3 - - - +
186A PHE* 1.3 63.3 + - - +
188A PHE* 3.9 1.1 - - - +
189A PHE* 3.0 21.6 + - - +
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Residues in contact with PHE 186 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64A PHE* 3.6 30.7 - + + -
152A LEU* 3.2 47.3 - - + -
155A LEU* 4.3 8.3 - - + -
156A PHE* 3.7 21.3 - + + -
159A TYR* 3.2 41.1 - + + +
182A SER 2.8 9.0 + - - +
183A PHE 3.1 7.4 + - - +
185A HIS* 1.3 74.4 - - - +
187A ILE* 1.3 76.8 + - + +
189A PHE* 3.2 0.9 + - - +
190A VAL* 3.0 34.4 + - + +
196A ILE* 3.5 23.3 - - + -
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Residues in contact with ILE 187 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156A PHE* 4.2 12.6 - - + -
183A PHE* 2.8 59.4 + - + +
184A LYS* 4.2 4.0 - - - +
186A PHE* 1.3 86.9 - - + +
188A PHE* 1.3 59.2 + - + +
190A VAL* 3.3 5.9 - - + +
191A GLN* 2.8 63.3 + - + +
201A LEU* 4.2 14.4 - - + -
208A ILE* 4.2 19.1 - - + -
211A LEU* 6.5 1.1 - - + -
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Residues in contact with PHE 188 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A LEU* 3.5 31.4 - - + +
42A ARG* 3.1 65.6 - - + +
45A VAL* 4.1 5.1 - - + +
184A LYS* 3.0 56.8 + - + +
185A HIS 3.9 2.2 - - - +
187A ILE* 1.3 76.5 - - + +
189A PHE* 1.3 62.7 + - - +
191A GLN* 3.6 12.5 - - - +
192A GLU* 3.0 23.0 + - - +
211A LEU* 4.4 21.8 - - + -
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Residues in contact with PHE 189 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45A VAL* 3.7 30.4 - - + +
56A TRP* 3.2 30.1 - + - -
57A ILE* 3.4 37.5 - - + -
60A ASN* 3.6 32.5 - - + -
61A THR 5.2 0.7 - - - -
64A PHE* 3.5 24.0 - + + -
152A LEU* 5.1 3.4 - - + -
185A HIS* 3.0 19.7 + - - +
186A PHE 3.6 2.5 - - - +
188A PHE* 1.3 76.3 - - - +
190A VAL* 1.3 72.1 + - + +
192A GLU* 3.0 11.4 + - - +
193A PHE* 3.1 28.8 + + - -
195A LEU* 4.3 11.0 - - + -
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Residues in contact with VAL 190 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64A PHE* 5.2 0.4 - - + -
152A LEU* 4.4 14.6 - - + -
186A PHE* 3.0 33.4 + - + +
187A ILE* 3.3 20.6 - - + +
189A PHE* 1.3 86.8 - - + +
191A GLN* 1.3 60.3 + - + +
193A PHE 4.6 0.2 - - - +
194A ASN* 2.7 31.0 + - - -
195A LEU* 3.2 16.3 + - + +
196A ILE* 4.2 43.7 + - + +
201A LEU* 5.3 3.8 - - + -
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Residues in contact with GLN 191 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42A ARG* 4.8 9.5 + - - -
187A ILE* 2.8 45.7 + - + +
188A PHE* 3.6 18.7 - - - +
190A VAL* 1.3 78.7 - - + +
192A GLU* 1.3 66.2 + - - +
194A ASN* 3.2 18.2 - - - +
201A LEU* 4.9 10.8 - - + +
208A ILE* 4.1 19.8 + - - +
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Residues in contact with GLU 192 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42A ARG* 4.5 5.9 - - - +
45A VAL* 4.2 9.9 - - + -
46A MET* 3.5 40.2 - - - +
47A LEU 4.9 1.0 + - - -
188A PHE 3.0 14.2 + - - +
189A PHE 3.0 8.0 + - - +
191A GLN* 1.3 78.6 - - - +
193A PHE* 1.3 84.6 + - + +
194A ASN* 3.9 6.4 + - - +
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Residues in contact with PHE 193 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45A VAL 3.2 24.0 - - - -
47A LEU* 3.9 22.0 - - + -
53A LEU* 4.0 26.2 - - + -
56A TRP* 3.4 21.5 - + - -
57A ILE* 3.5 19.5 - - + -
145A MET* 3.9 11.0 - - + +
189A PHE* 3.1 37.0 + + - +
192A GLU* 1.3 91.4 - - + +
194A ASN* 1.3 74.8 + - - +
195A LEU* 3.0 26.6 - - + +
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Residues in contact with ASN 194 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145A MET* 5.2 2.4 - - - +
149A LYS* 5.6 0.5 - - - +
190A VAL 2.7 16.2 + - - -
191A GLN* 3.2 14.8 + - - +
192A GLU 4.3 5.0 + - - +
193A PHE* 1.3 77.9 + - - +
195A LEU* 1.3 59.6 + - - +
196A ILE 3.5 6.9 - - - +
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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