Contacts of the helix formed by residues 160 - 179 (chain B) in PDB entry 1FBA
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 TYR 160 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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0A ACE 3.9 29.1 + - + +
1A THR* 3.5 11.7 + - - +
214A LYS* 4.8 5.7 + - - -
218A ASP* 4.1 28.7 + - + -
159B SER* 1.3 72.8 - - - +
161B GLN* 1.3 67.9 + - - +
163B ILE* 3.9 6.7 - - + -
164B LEU* 2.9 52.9 + - + +
0C ACE 4.1 26.4 + - + +
214C LYS* 5.7 4.3 - - - -
160D TYR* 3.4 52.9 + + + -
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Residues in contact with GLN 161 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A THR* 3.0 14.1 + - + +
218A ASP* 3.5 24.9 - - - +
219A HIS* 3.2 40.2 + - + +
220A HIS* 3.6 21.1 + - - +
115B LEU* 4.1 24.4 - - + +
116B PHE 4.8 3.0 + - - +
118B SER* 3.8 25.3 - - - +
159B SER* 3.1 7.8 + - - +
160B TYR* 1.3 81.5 - - - +
162B SER* 1.3 56.5 + - - +
164B LEU* 3.7 7.1 - - + +
165B GLU* 2.9 29.8 + - - +
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Residues in contact with SER 162 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115B LEU* 4.2 9.9 - - - -
121B GLU* 3.1 41.4 + - - +
122B VAL 4.2 4.0 + - - -
150B VAL 4.9 0.7 + - - -
151B LEU* 3.1 23.5 - - - +
152B LYS 5.8 0.2 + - - -
158B PRO* 4.5 0.7 - - - -
159B SER* 3.2 8.1 + - - -
161B GLN* 1.3 79.3 - - - +
163B ILE* 1.3 58.5 + - - +
165B GLU* 4.7 0.2 - - - -
166B ASN* 2.9 45.6 + - - +
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Residues in contact with ILE 163 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151B LEU* 4.8 6.3 - - + -
158B PRO* 3.9 31.4 - - + +
159B SER 3.0 20.9 + - - +
160B TYR* 3.9 6.1 - - + +
162B SER* 1.3 77.4 - - - +
164B LEU* 1.3 61.6 + - - +
166B ASN* 4.5 0.6 - - - +
167B ALA* 3.0 28.8 + - - +
207B THR* 3.9 31.6 - - + +
208B VAL* 4.4 16.8 - - + +
211B ALA* 3.3 30.1 - - + -
0C ACE 4.5 14.1 - - + +
2C THR* 4.2 7.9 - - + -
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Residues in contact with LEU 164 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164A LEU* 5.0 15.9 - - + -
168A ASN* 4.3 18.6 - - - +
218A ASP* 4.0 30.7 - - + +
219A HIS* 4.6 4.5 - - + +
160B TYR* 2.9 46.9 + - + +
161B GLN* 3.7 6.3 - - - +
163B ILE* 1.3 78.6 - - - +
165B GLU* 1.3 59.6 + - - +
167B ALA* 3.8 3.7 - - - +
168B ASN* 3.0 33.8 + - + +
211B ALA* 5.6 1.3 - - - -
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Residues in contact with GLU 165 (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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168A ASN* 3.0 29.1 + - - +
172A ARG* 3.7 19.4 + - - +
219A HIS* 4.1 10.7 - - + -
115B LEU* 4.1 13.9 - - + -
123B THR* 2.7 42.5 + - + +
161B GLN 2.9 18.3 + - - +
162B SER* 4.1 3.6 - - - +
164B LEU* 1.3 77.4 - - - +
166B ASN* 1.3 60.3 + - - +
168B ASN* 3.2 3.9 + - - +
169B VAL* 2.9 38.7 + - - +
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Residues in contact with ASN 166 (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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115B LEU* 4.9 0.2 - - - +
122B VAL 3.0 22.3 + - - +
123B THR* 3.5 21.7 + - - +
124B THR 4.1 0.3 + - - -
149B CYS* 3.4 32.3 - - + +
150B VAL 4.2 4.6 + - - -
151B LEU* 3.7 18.0 - - + +
162B SER* 2.9 39.5 + - - +
163B ILE 4.5 1.1 - - - +
165B GLU* 1.3 78.0 - - - +
167B ALA* 1.3 62.6 + - - +
169B VAL* 3.4 5.6 - - - +
170B LEU* 3.0 34.2 + - + +
188B PRO* 6.5 0.4 - - + -
212B VAL* 5.6 0.2 - - - -
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Residues in contact with ALA 167 (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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163B ILE 3.0 19.6 + - - +
164B LEU* 3.8 4.9 - - - +
166B ASN* 1.3 79.5 - - - +
168B ASN* 1.3 60.9 + - - +
170B LEU* 3.5 2.9 + - - +
171B ALA 3.2 16.6 + - - -
211B ALA* 3.6 37.5 - - + +
212B VAL* 3.9 17.2 - - + +
215B ALA* 3.3 16.1 - - + +
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Residues in contact with ASN 168 (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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164A LEU* 4.4 17.0 - - - +
165A GLU* 3.0 26.7 + - - +
168A ASN* 3.9 25.3 - - - +
164B LEU* 3.0 23.5 + - + +
165B GLU* 3.2 6.9 + - - +
167B ALA* 1.3 74.1 - - - +
169B VAL* 1.3 67.3 + - - +
171B ALA* 3.1 4.6 + - - +
172B ARG* 3.0 25.8 + - - +
215B ALA* 4.2 7.3 - - + +
219B HIS* 2.8 25.7 + - - -
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Residues in contact with VAL 169 (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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127A LEU* 6.6 0.4 - - + -
123B THR* 3.8 12.1 - - - +
124B THR 3.6 19.5 - - - +
127B LEU* 4.0 20.8 - - + +
147B TRP* 3.9 16.6 - - + +
149B CYS* 3.6 21.3 - - - -
165B GLU* 2.9 26.8 + - - +
166B ASN* 3.4 11.0 - - - +
168B ASN* 1.3 78.5 - - - +
170B LEU* 1.3 65.4 + - - +
172B ARG* 3.2 5.9 + - - +
173B TYR* 3.0 25.0 + - - +
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Residues in contact with LEU 170 (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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147B TRP* 3.7 28.0 - - + +
149B CYS* 3.5 17.3 - - + -
166B ASN* 3.0 23.7 + - + +
167B ALA* 3.8 4.5 - - - +
169B VAL* 1.3 79.1 - - - +
171B ALA* 1.3 57.0 + - - +
173B TYR* 3.4 16.3 + - + -
174B ALA* 2.9 28.1 + - - +
186B VAL* 4.2 17.1 - - + +
187B GLU 3.9 20.9 - - - +
188B PRO* 3.8 33.7 - - + -
212B VAL* 4.2 13.2 - - + -
216B LEU* 4.6 3.1 - - + +
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Residues in contact with ALA 171 (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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167B ALA 3.2 13.3 + - - +
168B ASN 3.1 5.6 + - - +
170B LEU* 1.3 72.6 - - - +
172B ARG* 1.3 61.7 + - - +
175B SER* 3.0 30.5 + - - -
215B ALA 3.5 17.5 - - - +
216B LEU* 3.7 17.0 - - + +
219B HIS* 3.4 34.6 - - + +
221B VAL* 3.8 4.5 - - - +
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Residues in contact with ARG 172 (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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113A VAL* 3.7 14.8 - - - +
114A PRO 4.8 5.9 + - - -
115A LEU* 3.8 15.0 - - - +
116A PHE 5.5 0.4 - - - +
123A THR* 3.4 25.4 - - - +
165A GLU* 3.7 37.7 + - - +
127B LEU* 3.8 30.4 - - + +
168B ASN* 3.0 20.7 + - - +
169B VAL* 3.2 8.5 + - - +
171B ALA* 1.3 75.4 - - - +
173B TYR* 1.3 65.8 + - - +
175B SER* 3.4 12.5 + - - -
176B ILE* 3.1 54.8 + - - +
219B HIS* 3.9 16.2 + - + -
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Residues in contact with TYR 173 (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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108B VAL* 3.6 15.5 - - + -
127B LEU* 3.8 10.9 - - + +
130B LEU* 4.3 6.9 - - + +
145B ALA* 3.1 23.7 + - + -
146B LYS* 3.5 1.0 + - - -
147B TRP* 3.4 55.2 - + + -
169B VAL 3.0 16.4 + - - +
170B LEU* 3.4 16.2 - - + -
172B ARG* 1.3 77.4 - - - +
174B ALA* 1.3 71.0 + - + +
176B ILE* 3.3 4.0 + - - +
177B CYS* 3.1 39.5 + - - -
184B PRO* 3.5 16.6 - - + +
185B ILE 2.9 33.9 + - - -
186B VAL* 4.5 6.1 - - + -
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Residues in contact with ALA 174 (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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170B LEU 2.9 16.7 + - - +
171B ALA 4.0 2.9 - - - +
172B ARG 3.3 0.2 - - - -
173B TYR* 1.3 78.2 - - + +
175B SER* 1.3 63.9 + - - +
177B CYS* 3.3 2.4 + - - +
178B GLN* 3.0 30.3 + - - +
184B PRO* 3.7 29.8 - - + +
186B VAL* 4.5 7.2 - - + -
216B LEU* 4.3 8.3 - - + -
221B VAL* 4.0 19.1 - - + -
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Residues in contact with SER 175 (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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116A PHE* 3.4 36.6 + - - +
171B ALA 3.0 19.1 + - - -
172B ARG* 3.5 15.8 + - - -
174B ALA* 1.3 76.0 - - - +
176B ILE* 1.3 63.6 + - - +
178B GLN* 3.3 5.4 + - - -
179B SER* 3.0 23.8 + - - -
219B HIS* 4.4 11.0 + - - +
221B VAL* 3.9 15.8 - - - +
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Residues in contact with ILE 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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113A VAL* 5.7 2.9 - - + -
114A PRO 5.7 3.1 - - - +
116A PHE* 5.8 0.9 - - + -
127B LEU* 4.4 16.8 - - + +
130B LEU* 3.7 31.2 - - + +
131B ALA* 3.5 37.9 - - + +
134B CYS* 4.8 1.6 - - - -
172B ARG* 3.1 47.0 + - - +
173B TYR 3.7 3.8 - - - +
174B ALA 3.2 0.2 - - - -
175B SER* 1.3 78.3 - - - +
177B CYS* 1.3 67.6 - - - +
179B SER* 2.6 26.0 + - - +
180B GLN* 3.3 5.7 + - - +
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Residues in contact with CYS 177 (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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108B VAL* 4.9 1.1 - - - -
130B LEU* 5.0 1.6 - - - -
134B CYS* 4.1 22.4 - - - -
145B ALA* 3.8 18.6 - - - -
173B TYR* 3.1 47.8 + - - +
174B ALA 3.3 6.9 + - - +
176B ILE* 1.3 75.4 - - - +
178B GLN* 1.3 63.5 + - - +
180B GLN* 2.9 14.8 + - - +
182B ILE* 3.0 36.4 + - + +
184B PRO* 4.0 7.9 - - + -
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Residues in contact with GLN 178 (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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116A PHE* 4.2 14.3 - - + -
7B PRO* 5.2 1.1 - - + +
11B LEU* 3.5 20.1 - - - +
15B LEU* 3.7 18.5 - - + +
174B ALA 3.0 21.5 + - - +
175B SER* 3.8 5.3 - - - +
177B CYS* 1.3 74.6 - - - +
179B SER* 1.3 61.5 + - - +
180B GLN 3.2 0.5 + - - -
181B ARG* 3.2 9.2 + - - -
182B ILE 3.7 4.5 - - - +
184B PRO* 3.8 13.9 - - + -
220B HIS 5.0 0.3 - - - +
221B VAL* 3.7 12.1 - - - +
222B TYR* 2.7 56.6 + - - +
225B GLY* 3.2 20.4 + - - -
226B THR* 3.4 5.9 - - - +
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Residues in contact with SER 179 (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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116A PHE* 3.7 39.3 - - - -
11B LEU* 4.7 5.7 - - - +
131B ALA* 4.8 2.1 - - - +
175B SER 3.0 14.0 + - - -
176B ILE* 2.6 24.5 + - - +
178B GLN* 1.3 75.8 - - - +
180B GLN* 1.3 80.8 + - - +
181B ARG* 3.4 3.9 + - - +
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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