Contacts of the helix formed by residues 161 - 174 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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31B THR* 4.7 15.5 - - + -
32B ASP* 5.8 2.5 - - - +
33B THR* 5.8 2.5 - - - +
160B ARG* 1.3 84.8 - - + +
162B LYS* 1.3 66.9 + - - +
163B GLY 4.5 2.9 - - - +
164B GLU* 2.9 43.3 + - + +
165B LEU* 3.1 13.4 + - - +
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Residues in contact with LYS 162 (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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25A LEU* 4.1 30.7 - - + -
77A GLU* 4.9 9.9 - - - +
78A HIS* 2.8 43.8 + - + +
160B ARG 3.8 2.0 + - - -
161B LEU* 1.3 71.3 - - - +
163B GLY* 1.3 59.6 + - - +
165B LEU* 3.4 8.8 + - - +
166B ALA* 3.0 28.7 + - + +
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Residues in contact with GLY 163 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A SER* 6.2 0.4 - - - -
30B TRP* 3.5 37.6 - - - +
31B THR* 3.9 11.2 - - - +
161B LEU* 3.3 1.2 - - - +
162B LYS* 1.3 82.9 - - - +
164B GLU* 1.3 55.6 + - - +
166B ALA* 3.5 8.1 + - - +
167B TYR* 3.1 21.3 + - - +
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Residues in contact with GLU 164 (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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30B TRP* 5.5 0.7 - - - -
31B THR* 4.1 5.1 + - + +
33B THR* 5.2 2.4 + - - -
34B LEU* 3.4 33.3 - - + +
82B PHE* 5.7 3.0 - - + -
158B THR 4.5 1.6 - - - +
159B CYS* 3.5 28.0 - - + -
160B ARG* 3.0 24.1 + - - +
161B LEU* 2.9 39.2 + - + +
163B GLY* 1.3 75.5 - - - +
165B LEU* 1.3 65.5 + - - +
167B TYR* 3.4 8.4 + - - +
168B MET* 3.3 23.6 + - - +
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Residues in contact with LEU 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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157B HIS* 4.2 6.1 - - + +
159B CYS* 4.2 17.9 - - + +
160B ARG* 4.0 20.0 - - - +
161B LEU 3.1 11.1 + - - +
162B LYS* 3.8 9.2 - - - +
164B GLU* 1.3 76.0 - - - +
166B ALA* 1.3 58.4 + - - +
168B MET* 3.3 26.4 + - + +
169B ASP* 2.9 30.2 + - - +
193B PRO* 6.2 0.7 - - + -
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Residues in contact with ALA 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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78A HIS* 6.5 0.9 - - + -
170A TYR* 5.8 1.8 - - + -
30B TRP* 4.1 16.7 - - + -
162B LYS* 3.0 20.4 + - + +
163B GLY* 3.7 9.2 - - - +
164B GLU 3.3 0.2 - - - -
165B LEU* 1.3 75.4 - - - +
167B TYR* 1.3 57.6 + - - +
169B ASP* 3.3 7.3 + - - +
170B TYR* 2.9 29.8 + - - +
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Residues in contact with TYR 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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30B TRP* 3.2 38.1 - + + -
36B SER* 3.6 17.1 - - - -
71B VAL* 3.4 15.3 - - + +
80B GLU* 2.6 31.4 + - - +
82B PHE* 3.2 53.3 - + + +
134B LEU* 4.5 14.6 - - + -
138B MET* 4.6 3.4 - - + -
163B GLY 3.1 13.5 + - - +
164B GLU* 3.5 10.5 - - - +
165B LEU 3.2 0.2 - - - -
166B ALA* 1.3 76.1 - - - +
168B MET* 1.3 59.8 + - + +
170B TYR* 3.2 13.0 + + - +
171B ILE* 2.9 43.0 + - + +
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Residues in contact with MET 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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134B LEU* 4.3 17.0 - - + -
138B MET* 4.0 23.5 - - - +
155B LEU* 4.6 2.2 - - - -
157B HIS* 3.5 42.6 - - + +
159B CYS* 3.7 19.7 - - + -
164B GLU 3.3 8.2 + - - +
165B LEU* 3.3 19.4 + - + +
167B TYR* 1.3 79.5 - - + +
169B ASP* 1.3 61.4 + - - +
171B ILE* 3.4 8.0 + - - +
172B LYS* 3.2 24.8 + - - +
191B TYR* 4.1 31.6 + - + -
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Residues in contact with ASP 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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173A HIS 3.7 19.2 - - - +
174A ASP* 4.6 8.7 - - - +
175A LEU 5.0 0.9 + - - -
179A GLU* 4.5 12.1 - - - +
165B LEU 2.9 17.7 + - - +
166B ALA* 3.7 7.4 - - - +
168B MET* 1.3 73.9 - - - +
170B TYR* 1.3 65.5 + - - +
172B LYS* 3.5 28.3 + - - +
173B HIS* 3.2 33.0 + - - -
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Residues in contact with TYR 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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30A TRP* 5.4 9.9 - + - -
166A ALA 6.0 0.2 - - - -
170A TYR* 4.2 38.6 - + + -
173A HIS* 6.5 0.2 - - - -
28B HIS* 5.8 6.9 + + - -
30B TRP* 4.1 20.9 - + + -
36B SER* 5.6 0.2 - - - -
38B THR* 4.9 5.4 - - - +
78B HIS* 5.3 2.1 + - - -
80B GLU* 2.8 37.6 + - - -
166B ALA 2.9 16.5 + - - +
167B TYR* 3.7 21.1 - + - -
169B ASP* 1.3 76.4 - - - +
171B ILE* 1.3 82.9 + - + +
172B LYS 3.2 0.5 + - - -
173B HIS* 3.2 14.4 + - - +
174B ASP* 3.4 28.1 + - + +
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Residues in contact with ILE 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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71B VAL* 3.6 23.6 - - + -
80B GLU* 3.8 9.6 - - - +
138B MET* 3.7 33.7 - - + +
141B ILE* 4.6 4.5 - - + -
142B ARG* 3.5 40.9 + - - +
167B TYR* 2.9 40.7 + - + +
168B MET 3.7 5.2 - - - +
170B TYR* 1.3 93.0 - - + +
172B LYS* 1.3 68.0 + - - +
174B ASP* 2.9 14.3 + - - -
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Residues in contact with LYS 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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179A GLU* 5.6 4.8 + - - -
141B ILE* 4.5 8.5 - - + -
142B ARG* 4.9 2.5 - - - +
168B MET 3.2 9.0 + - - +
169B ASP* 3.5 31.4 + - - +
170B TYR 3.2 0.6 + - - -
171B ILE* 1.3 82.3 - - - +
173B HIS* 1.3 83.3 + - + +
174B ASP 3.4 0.2 - - - -
175B LEU* 3.8 20.5 - - - +
185B ILE* 4.0 26.2 - - + +
186B ARG* 6.3 2.5 - - - +
191B TYR* 3.3 41.3 - - + +
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Residues in contact with HIS 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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169A ASP* 4.2 5.4 - - - +
173A HIS* 3.5 70.9 + - + +
179A GLU* 4.6 13.1 + - - -
169B ASP* 3.2 32.2 + - - -
170B TYR* 3.2 6.9 + - - +
171B ILE 3.1 0.8 - - - -
172B LYS* 1.3 103.7 + - + +
174B ASP* 1.3 60.6 + - - +
175B LEU* 3.1 19.0 + - - +
179B GLU* 4.8 4.3 - - - +
182B GLY* 6.1 2.6 - - - -
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Residues in contact with ASP 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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169A ASP* 5.0 8.1 - - - +
73B PRO* 5.2 0.2 - - - +
75B TYR* 5.1 0.2 + - - -
76B GLU* 2.6 32.9 - - - +
78B HIS* 4.8 2.0 + - - -
80B GLU* 4.5 1.7 - - - +
142B ARG* 3.0 47.9 + - - +
170B TYR* 3.4 36.2 + - + +
171B ILE 2.9 7.1 + - - +
173B HIS* 1.3 75.9 - - - +
175B LEU* 1.3 57.1 + - - +
176B PRO* 3.5 8.2 - - - +
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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