Contacts of the helix formed by residues 160 - 170 (chain A) in PDB entry 1TF5
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 SER 160 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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158A SER 4.0 1.8 + - - -
159A MET* 1.3 76.8 - - - +
161A LYS* 1.3 59.5 + - - +
162A ASP* 3.6 7.4 + - - +
163A GLU* 3.3 24.1 + - - +
164A LYS* 2.8 27.6 + - - +
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Residues in contact with LYS 161 (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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160A SER* 1.3 72.7 - - - +
162A ASP* 1.3 61.0 + - - +
164A LYS* 3.1 11.2 + - + +
165A ARG* 2.8 45.0 + - - +
186A ARG* 3.8 41.6 + - - +
190A VAL* 5.8 4.9 - - - +
195A GLN* 5.0 7.3 + - - +
197A VAL* 3.8 18.9 - - + +
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Residues in contact with ASP 162 (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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160A SER* 3.3 7.4 + - - +
161A LYS* 1.3 77.5 - - - +
163A GLU* 1.3 64.0 + - - +
165A ARG* 3.0 27.6 + - - +
166A GLU* 3.1 22.5 + - - +
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Residues in contact with GLU 163 (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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158A SER 5.3 0.2 - - - +
159A MET* 3.1 58.1 - - + +
160A SER* 3.2 19.5 + - - +
162A ASP* 1.3 79.3 - - - +
164A LYS* 1.3 57.1 + - - +
166A GLU* 3.5 7.5 + - + +
167A ALA 3.1 20.8 + - - -
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Residues in contact with LYS 164 (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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155A ASN* 2.9 33.8 + - - +
156A LEU 3.5 10.0 + - - -
157A ASN 4.7 3.4 - - - -
159A MET* 3.5 29.2 - - + +
160A SER 2.8 19.8 + - - +
161A LYS* 3.4 13.9 - - + +
163A GLU* 1.3 73.6 - - - +
165A ARG* 1.3 61.7 + - - +
167A ALA* 3.2 5.5 + - - +
168A TYR* 2.9 38.2 + - + -
179A GLU* 3.0 25.4 + - - -
183A ASP* 3.0 26.1 + - - +
186A ARG* 4.2 15.3 - - - +
197A VAL* 4.3 9.9 - - + -
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Residues in contact with ARG 165 (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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161A LYS* 2.8 19.5 + - - +
162A ASP* 3.0 37.4 + - - +
164A LYS* 1.3 76.0 - - - +
166A GLU* 1.3 62.5 + - - +
168A TYR* 3.3 3.1 + - - +
169A ALA* 3.1 22.9 + - + +
194A GLU 3.3 18.5 + - - -
195A GLN* 2.9 29.9 + - - +
196A MET 2.8 19.5 + - - +
197A VAL* 3.8 22.7 - - - +
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Residues in contact with GLU 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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162A ASP 3.1 15.4 + - - +
163A GLU* 3.7 8.3 - - + +
164A LYS 3.2 0.2 - - - -
165A ARG* 1.3 78.1 - - - +
167A ALA* 1.3 61.7 + - - +
169A ALA* 3.0 25.2 + - - +
170A ALA* 3.3 10.4 + - - +
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Residues in contact with ALA 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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153A GLY* 3.8 9.5 - - - -
154A LEU 3.5 36.3 - - - +
155A ASN* 4.3 8.1 - - + +
159A MET* 4.1 3.6 - - + -
163A GLU 3.1 14.9 + - - +
164A LYS 3.2 8.9 + - - +
166A GLU* 1.3 75.2 - - - +
168A TYR* 1.3 59.4 + - - +
169A ALA 3.5 0.7 + - - -
170A ALA* 3.5 12.0 + - - +
173A THR* 2.8 22.2 + - + +
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Residues in contact with TYR 168 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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123A GLY* 5.6 0.2 - - - -
125A HIS* 3.6 36.8 + + - -
155A ASN* 3.4 17.4 + - + -
164A LYS* 2.9 27.2 + - + +
165A ARG 3.6 2.5 - - - +
166A GLU 3.1 0.2 - - - -
167A ALA* 1.3 75.8 - - - +
169A ALA* 1.3 57.0 + - - +
170A ALA 3.3 1.1 - - - +
173A THR* 3.8 11.7 + - + -
180A LEU* 3.1 19.9 - - + +
183A ASP* 2.8 30.1 + - - +
197A VAL* 3.2 38.4 - - + +
198A GLN* 3.1 36.7 + - + -
199A ARG* 3.0 31.2 + - + +
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Residues in contact with ALA 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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151A THR* 4.8 0.3 + - - -
165A ARG* 3.1 12.1 + - + +
166A GLU* 3.0 25.0 + - - +
168A TYR* 1.3 74.8 - - - +
170A ALA* 1.3 69.0 + - - +
171A ASP* 5.3 1.0 - - - +
199A ARG* 3.3 18.9 + - + +
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Residues in contact with ALA 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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123A GLY* 4.5 0.2 - - - -
151A THR* 3.3 28.9 - - - +
152A VAL 3.9 1.8 - - - +
153A GLY* 3.5 14.6 - - - +
166A GLU* 3.3 8.1 + - - +
167A ALA 3.6 7.9 - - - +
168A TYR 3.3 2.9 - - - +
169A ALA* 1.3 79.1 - - - +
171A ASP* 1.3 62.5 + - - +
172A ILE 3.2 14.1 - - - +
173A THR* 4.3 3.3 + - - -
199A ARG* 2.7 25.1 + - - -
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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