Contacts of the helix formed by residues 161 - 173 (chain A) in PDB entry 4FK8
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 LEU 161 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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31A THR* 4.8 14.8 - - + +
32A ASP* 5.9 2.5 - - - +
33A THR* 5.6 4.0 - - - +
160A ARG* 1.3 87.2 - - + +
162A LYS* 1.3 68.0 + - - +
163A GLY 4.4 3.8 - - - +
164A GLU* 2.9 44.0 + - + +
165A LEU* 3.1 12.9 + - - +
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Residues in contact with LYS 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 ARG 3.8 1.8 + - - -
161A LEU* 1.3 72.1 - - - +
163A GLY* 1.3 58.8 + - - +
165A LEU* 3.3 9.7 + - - +
166A ALA* 2.9 31.7 + - + +
25B LEU* 4.0 31.6 - - + -
77B GLU* 3.5 29.3 + - - +
78B HIS* 2.7 41.5 + - + +
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Residues in contact with GLY 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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30A TRP* 3.6 36.5 - - - +
31A THR* 3.7 13.0 - - - +
161A LEU* 3.3 1.4 - - - +
162A LYS* 1.3 77.7 - - - +
164A GLU* 1.3 64.2 + - - +
166A ALA* 3.8 8.3 - - - +
167A TYR* 3.2 16.5 + - - +
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Residues in contact with GLU 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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30A TRP* 5.6 0.4 - - - -
31A THR* 4.0 3.3 - - + +
33A THR* 5.4 1.0 + - - -
34A LEU* 3.5 34.3 - - + +
82A PHE* 5.7 4.3 - - + -
134A LEU* 5.8 0.2 - - - +
158A THR 4.5 2.2 - - - +
159A CYS* 3.6 27.3 - - + -
160A ARG* 2.9 11.8 + - - +
161A LEU* 2.9 49.9 + - + +
163A GLY* 1.3 75.9 - - - +
165A LEU* 1.3 63.4 + - - +
167A TYR* 3.3 8.5 + - - +
168A MET* 3.2 23.9 + - - +
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Residues in contact with LEU 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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157A HIS* 4.2 6.3 - - + +
159A CYS* 3.8 22.4 - - + +
160A ARG* 3.9 20.0 - - - +
161A LEU 3.1 11.8 + - - +
162A LYS* 3.8 8.5 - - - +
164A GLU* 1.3 79.3 - - - +
166A ALA* 1.3 60.0 + - - +
168A MET* 3.3 24.5 + - + +
169A ASP* 2.9 30.1 + - - +
193A PRO* 6.2 0.7 - - + -
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Residues in contact with ALA 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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30A TRP* 4.0 16.8 - - + -
162A LYS* 2.9 18.8 + - + +
163A GLY* 3.8 10.1 - - - +
165A LEU* 1.3 76.5 - - - +
167A TYR* 1.3 55.5 + - - +
169A ASP* 3.3 7.1 + - - +
170A TYR* 2.9 30.0 + - - +
78B HIS* 6.5 1.3 - - + -
170B TYR* 6.0 0.3 - - - -
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Residues in contact with TYR 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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30A TRP* 3.2 39.0 - + + -
36A SER* 3.6 17.0 - - - -
71A VAL* 3.4 16.0 - - + +
80A GLU* 2.7 31.2 + - - +
82A PHE* 3.2 53.8 - + + +
134A LEU* 4.7 6.7 - - + -
138A MET* 4.7 9.4 - - + -
163A GLY 3.2 13.7 + - - +
164A GLU* 3.5 10.3 - - - +
165A LEU 3.2 0.6 - - - -
166A ALA* 1.3 76.3 - - - +
168A MET* 1.3 65.1 + - + +
170A TYR* 3.3 8.5 + + - +
171A ILE* 3.0 38.2 + - + +
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Residues in contact with MET 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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134A LEU* 4.4 16.8 - - + -
138A MET* 4.1 25.2 - - - +
155A LEU* 4.6 3.4 - - - -
157A HIS* 3.6 43.5 - - + +
159A CYS* 3.8 18.2 - - + -
164A GLU 3.2 7.3 + - - +
165A LEU* 3.3 19.5 + - + +
167A TYR* 1.3 81.0 - - + +
169A ASP* 1.3 60.9 - - - +
171A ILE* 3.5 7.5 + - - +
172A LYS* 3.2 25.9 + - - +
191A TYR* 4.1 31.7 + - + -
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Residues in contact with ASP 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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165A LEU 2.9 18.4 + - - +
166A ALA* 3.7 7.6 - - - +
167A TYR 3.2 0.2 - - - -
168A MET* 1.3 75.8 - - - +
170A TYR* 1.3 64.9 + - - +
172A LYS* 3.2 34.6 + - - +
173A HIS* 3.2 29.6 + - - -
173B HIS 4.2 14.0 - - - +
174B ASP* 5.0 7.6 - - - +
175B LEU 5.3 1.0 + - - -
179B GLU* 5.0 8.9 - - - +
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Residues in contact with TYR 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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28A HIS* 5.6 7.3 + + - -
30A TRP* 3.9 28.3 - + + -
36A SER* 5.7 0.2 - - - -
38A THR* 5.1 4.2 - - - +
78A HIS* 5.6 1.2 + - - -
80A GLU* 3.1 27.8 + - - -
166A ALA 2.9 17.3 + - - +
167A TYR* 3.7 11.4 - + - -
169A ASP* 1.3 76.6 - - - +
171A ILE* 1.3 98.1 + - + +
173A HIS* 3.1 16.6 + - - +
174A ASP* 3.5 29.4 + - + -
30B TRP* 4.9 13.9 - + - -
166B ALA* 5.8 1.6 - - + -
170B TYR* 4.2 40.4 - + + -
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Residues in contact with ILE 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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71A VAL* 3.6 27.4 - - + -
80A GLU* 3.7 4.3 - - - +
138A MET* 3.6 32.5 - - + +
141A ILE* 4.8 3.6 - - + -
142A ARG* 3.5 38.5 + - - +
167A TYR* 3.0 42.8 + - + +
168A MET 3.7 4.7 - - - +
169A ASP 3.4 0.2 - - - -
170A TYR* 1.3 97.8 - - + +
172A LYS* 1.3 66.3 + - - +
174A ASP* 3.0 14.1 + - - -
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Residues in contact with LYS 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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141A ILE* 4.5 9.2 - - + -
142A ARG* 5.0 2.5 - - - +
168A MET 3.2 7.9 + - - +
169A ASP* 3.2 35.9 + - - +
170A TYR 3.2 0.4 + - - -
171A ILE* 1.3 81.9 - - - +
173A HIS* 1.3 80.4 + - + +
174A ASP 3.5 0.2 - - - -
175A LEU* 3.7 21.3 - - - +
182A GLY* 5.8 0.5 - - - -
185A ILE* 4.1 23.2 - - + +
191A TYR* 3.4 44.0 - - + +
179B GLU* 6.0 2.4 - - - -
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Residues in contact with HIS 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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169A ASP* 3.2 30.7 + - - -
170A TYR* 3.1 8.3 + - - +
171A ILE 3.1 0.8 - - - -
172A LYS* 1.3 105.2 + - + +
174A ASP* 1.3 57.7 + - - +
175A LEU* 3.2 17.3 + - - +
179A GLU* 4.9 3.6 - - - +
182A GLY* 6.0 3.6 - - - -
169B ASP* 3.7 13.3 - - - +
170B TYR* 6.5 0.2 - - - -
173B HIS* 3.5 63.9 + - + +
179B GLU* 4.8 12.3 + - - -
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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