Contacts of the helix formed by residues 165 - 183 (chain A) in PDB entry 3F5T
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 THR 165 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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135A ARG* 5.4 4.3 - - - -
137A GLU* 4.6 6.3 - - - +
164A HIS* 1.3 82.9 - - - +
166A GLY* 1.3 64.0 + - - +
167A GLU* 3.5 11.8 + - - +
168A ASP* 3.1 31.6 + - - +
169A VAL* 3.1 27.0 + - - +
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Residues in contact with GLY 166 (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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135A ARG* 4.3 10.6 - - - +
136A LEU* 3.5 39.2 + - - +
137A GLU 4.5 2.0 + - - -
165A THR* 1.3 73.4 - - - +
167A GLU* 1.3 51.7 + - - +
169A VAL* 3.2 5.5 + - - +
170A LYS* 2.8 34.8 + - - +
197A ALA* 5.7 1.6 - - - +
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Residues in contact with GLU 167 (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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135A ARG* 5.6 0.4 - - - +
165A THR* 3.5 10.3 - - - +
166A GLY* 1.3 72.0 - - - +
168A ASP* 1.3 68.2 + - - +
170A LYS* 2.5 37.0 + - - +
171A ASN* 2.9 34.8 + - - +
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Residues in contact with ASP 168 (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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107A ALA 5.4 6.1 - - - +
108A GLY* 6.1 4.0 - - - -
109A SER* 5.3 2.5 + - - +
110A LEU* 3.5 20.0 - - + +
163A GLY 4.9 1.4 - - - +
164A HIS* 3.8 9.8 - - + +
165A THR* 3.1 37.7 + - - +
167A GLU* 1.3 79.8 - - - +
169A VAL* 1.3 57.8 + - - +
171A ASN* 3.3 8.3 + - - +
172A ALA* 3.0 22.9 + - - +
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Residues in contact with VAL 169 (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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110A LEU* 3.6 17.0 - - + -
136A LEU* 3.9 33.2 - - + -
139A LEU* 4.0 20.2 - - + -
142A LEU* 6.2 0.2 - - + -
155A ILE* 6.3 0.7 - - + -
164A HIS* 3.5 25.1 - - + +
165A THR 3.1 12.7 + - - +
166A GLY 3.3 9.0 - - - +
167A GLU 3.1 0.6 - - - -
168A ASP* 1.3 76.8 - - - +
170A LYS* 1.3 65.8 + - - +
172A ALA* 3.2 3.7 + - - +
173A ILE* 3.1 38.5 + - + +
197A ALA* 5.0 3.1 - - + -
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Residues in contact with LYS 170 (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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166A GLY 2.8 14.7 + - - +
167A GLU* 2.5 37.8 + - - +
169A VAL* 1.3 78.6 - - - +
171A ASN* 1.3 77.9 + - - +
173A ILE* 3.5 10.2 + - - +
174A GLY* 3.2 18.5 + - - -
197A ALA* 4.6 26.7 - - + +
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Residues in contact with ASN 171 (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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167A GLU* 2.9 30.0 + - - +
168A ASP* 3.5 10.5 - - - +
170A LYS* 1.3 90.0 + - - +
172A ALA* 1.3 65.8 + - - +
174A GLY* 3.3 3.2 + - - -
175A VAL* 3.0 31.1 + - + +
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Residues in contact with ALA 172 (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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107A ALA* 5.9 1.6 - - + -
110A LEU* 3.9 16.8 - - + -
112A ILE* 3.6 30.6 - - + +
155A ILE* 3.8 16.7 - - + +
168A ASP 3.0 13.3 + - - +
169A VAL* 3.2 9.6 + - - +
171A ASN* 1.3 75.2 - - - +
173A ILE* 1.3 55.4 + - - +
175A VAL* 3.1 6.3 + - - +
176A LEU* 2.9 28.9 + - - +
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Residues in contact with ILE 173 (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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125A LEU* 4.0 10.9 - - + +
136A LEU* 6.0 0.9 - - + -
142A LEU* 3.8 29.4 - - + -
155A ILE* 3.9 10.8 - - + -
169A VAL* 3.1 30.4 + - + +
170A LYS* 3.8 7.6 - - - +
171A ASN 3.3 0.2 - - - -
172A ALA* 1.3 73.3 - - - +
174A GLY* 1.3 55.7 + - - +
176A LEU* 3.0 3.2 + - - +
177A ILE* 2.7 56.0 + - + +
189A VAL* 4.8 6.3 - - + -
193A ILE* 4.1 18.2 - - + -
197A ALA* 4.2 14.4 - - + -
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Residues in contact with GLY 174 (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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170A LYS 3.2 11.1 + - - -
171A ASN* 3.3 3.6 + - - -
173A ILE* 1.3 79.9 - - - +
175A VAL* 1.3 56.3 + - - +
177A ILE* 4.0 6.9 - - - +
178A GLY* 2.9 25.3 + - - -
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Residues in contact with VAL 175 (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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105A LYS* 4.9 20.6 - - + +
112A ILE* 4.8 15.0 - - + -
114A MET* 5.6 0.3 - - - +
171A ASN* 3.0 21.7 + - + +
172A ALA* 3.4 9.9 - - - +
174A GLY* 1.3 75.9 - - - +
176A LEU* 1.3 60.4 + - - +
178A GLY* 3.6 1.2 + - - -
179A GLY* 3.0 22.7 + - - -
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Residues in contact with LEU 176 (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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112A ILE* 4.4 11.7 - - + -
113A LYS 3.9 10.3 - - - +
114A MET* 3.8 31.2 - - + -
125A LEU* 4.1 17.7 - - + -
142A LEU* 3.9 17.9 - - + -
144A ALA* 4.8 2.7 - - + -
153A GLY* 4.5 2.9 - - - -
154A GLU 4.8 7.4 - - - +
155A ILE* 3.8 27.1 - - + -
172A ALA 2.9 15.0 + - - +
173A ILE 3.6 2.9 - - - +
175A VAL* 1.3 75.7 - - - +
177A ILE* 1.3 65.4 + - - +
179A GLY* 3.3 1.1 + - - +
180A LEU* 3.1 35.3 + - + +
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Residues in contact with ILE 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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125A LEU* 3.9 19.5 - - + -
173A ILE* 2.7 40.5 + - + +
174A GLY* 4.0 6.7 - - - +
176A LEU* 1.3 72.0 - - - +
178A GLY* 1.3 64.7 + - - +
180A LEU* 3.3 1.8 + - - +
181A GLU* 3.0 49.3 + - + +
187A VAL* 4.0 22.7 - - + +
188A ARG* 5.7 1.3 - - - -
189A VAL* 4.3 12.6 - - + -
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Residues in contact with GLY 178 (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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174A GLY 2.9 19.8 + - - -
175A VAL* 3.8 2.2 - - - -
176A LEU 3.2 0.4 - - - -
177A ILE* 1.3 80.0 - - - +
179A GLY* 1.3 61.0 + - - +
181A GLU* 3.2 15.6 + - - +
182A TRP* 3.3 13.0 + - - +
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Residues in contact with GLY 179 (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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103A LYS* 4.4 13.4 + - - -
114A MET* 3.6 29.2 - - - +
175A VAL 3.0 15.5 + - - -
176A LEU 3.3 0.2 + - - -
178A GLY* 1.3 73.8 - - - +
180A LEU* 1.3 61.5 + - - +
181A GLU 3.4 0.3 + - - -
182A TRP* 3.4 18.8 + - - +
183A ASN* 4.3 3.3 + - - -
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Residues in contact with LEU 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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114A MET* 3.8 18.6 - - + -
115A ASP 4.7 5.6 - - - +
118A ILE* 5.2 2.2 - - + +
123A ILE* 3.9 41.3 - - + -
125A LEU* 4.4 0.7 - - + -
144A ALA* 4.3 9.0 - - + -
152A VAL* 4.3 21.3 - - + +
176A LEU* 3.1 38.0 + - + +
177A ILE 3.8 3.1 - - - +
179A GLY* 1.3 77.1 - - - +
181A GLU* 1.3 61.0 + - - +
183A ASN* 3.4 6.3 + - - +
185A ASN* 2.9 33.0 + - - +
187A VAL* 3.9 21.5 - - + -
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Residues in contact with GLU 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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177A ILE* 3.0 37.9 + - - +
178A GLY* 3.2 7.1 + - - +
180A LEU* 1.3 76.3 - - - +
182A TRP* 1.3 67.0 + - - +
184A ASP* 2.9 16.1 + - - +
185A ASN 3.5 21.2 - - - +
186A THR* 5.5 0.3 - - - -
187A VAL* 3.9 20.3 + - + +
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Residues in contact with TRP 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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178A GLY 3.3 9.4 + - - +
179A GLY* 3.5 14.6 - - - +
181A GLU* 1.3 77.6 - - - +
183A ASN* 1.3 68.8 + - - +
184A ASP* 3.1 13.9 + - - +
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Residues in contact with ASN 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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114A MET* 4.8 7.9 - - - +
116A GLN* 2.9 37.4 + - - +
118A ILE 3.3 22.1 + - - +
119A MET* 3.4 27.7 - - + +
120A ASP 3.3 14.6 + - - -
179A GLY 4.9 2.2 + - - -
180A LEU 3.4 2.8 + - - +
181A GLU 3.2 1.2 - - - -
182A TRP* 1.3 87.0 - - - +
184A ASP* 1.3 74.8 + - - +
185A ASN* 3.2 7.6 + - - +
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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