Contacts of the helix formed by residues 173 - 184 (chain A) in PDB entry 4HK4
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 GLN 173 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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34A GLY 5.7 2.5 - - - -
137A ILE* 4.0 19.8 - - - +
151A TYR* 5.1 2.2 + - - -
155A GLN* 3.1 35.0 + - - +
169A GLY* 4.5 4.3 - - - -
170A GLY 3.0 23.5 + - - +
172A GLU* 1.3 103.8 + - - +
174A ARG* 1.3 63.9 + - - +
175A LYS 3.2 2.7 - - - -
176A ILE* 3.1 8.6 + - - +
177A HIS* 3.0 41.9 + - + +
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Residues in contact with ARG 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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13A GLU* 3.0 33.7 + - - +
15A ILE* 5.2 4.6 - - - +
136A LEU* 5.8 4.5 - - + -
170A GLY 4.0 0.8 + - - -
171A MET* 3.3 35.8 + - - +
172A GLU 3.3 1.2 - - - -
173A GLN* 1.3 78.2 - - - +
175A LYS* 1.3 69.5 + - + +
177A HIS* 3.8 1.4 - - - +
178A MET* 2.9 57.1 + - + +
192A HIS* 3.4 28.2 - - + +
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Residues in contact with LYS 175 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129A ARG* 4.9 2.8 + - - -
132A ARG* 3.3 50.0 + - - +
133A SER* 3.5 22.0 - - - +
135A GLU* 3.1 26.6 + - + +
136A LEU* 6.3 6.5 - - + -
172A GLU 4.6 2.6 + - - +
173A GLN 3.2 0.8 - - - -
174A ARG* 1.3 84.6 - - + +
176A ILE* 1.3 60.7 + - - +
178A MET* 3.5 23.1 + - + +
179A LEU* 3.0 27.2 + - - +
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Residues in contact with ILE 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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133A SER* 3.5 27.3 + - - +
134A MET* 4.3 1.3 - - - -
137A ILE* 3.4 29.8 - - + -
151A TYR* 3.9 16.8 - - + -
152A PRO* 4.0 30.1 - - + +
155A GLN* 3.5 30.3 - - + +
156A VAL* 3.7 8.0 - - + +
159A ILE* 5.6 1.3 - - + -
173A GLN* 3.1 9.3 + - - +
175A LYS* 1.3 77.1 - - - +
177A HIS* 1.3 61.9 + - + +
179A LEU* 3.2 7.9 - - - +
180A ALA* 2.9 25.5 + - - +
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Residues in contact with HIS 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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32A GLU* 5.1 2.4 + - - -
155A GLN* 4.8 3.5 + - - -
159A ILE* 3.8 27.7 - - + +
167A ALA* 4.0 24.2 + - + +
168A VAL 4.2 16.4 + - - -
169A GLY* 4.3 0.7 - - - -
173A GLN* 3.0 35.6 + - + +
174A ARG 3.8 4.5 - - - +
176A ILE* 1.3 81.9 - - + +
178A MET* 1.3 60.6 + - - +
180A ALA* 3.2 6.4 + - - +
181A ARG* 3.0 30.7 + - - +
188A VAL* 6.0 0.2 - - + -
190A CYS* 3.6 20.9 - - - -
192A HIS* 2.8 31.7 + + + +
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Residues in contact with MET 178 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A ILE* 6.2 5.4 - - + -
129A ARG* 4.6 6.7 - - - +
132A ARG* 4.8 12.6 - - - +
174A ARG* 2.9 45.8 + - + +
175A LYS* 3.6 36.8 - - + +
176A ILE 3.3 0.2 - - - -
177A HIS* 1.3 73.6 - - + +
179A LEU* 1.3 66.1 + - - +
181A ARG* 3.3 14.9 + - - +
182A GLU* 3.2 30.4 + - - +
192A HIS* 6.1 1.6 - - + -
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Residues in contact with LEU 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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125A THR* 4.2 26.2 - - + -
129A ARG* 4.0 34.9 - - + +
130A ALA* 5.1 0.9 - - - -
133A SER* 4.4 19.3 - - - +
152A PRO* 4.5 16.4 - - + +
153A ILE* 5.4 1.1 - - + -
156A VAL* 4.2 7.9 - - + -
175A LYS 3.0 13.6 + - - +
176A ILE* 3.2 11.4 - - - +
178A MET* 1.3 77.0 - - - +
180A ALA* 1.3 55.9 + - - +
182A GLU* 3.0 8.9 + - - +
183A LEU* 2.9 60.1 + - + +
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Residues in contact with ALA 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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156A VAL* 3.9 25.5 - - + +
159A ILE* 4.1 18.8 - - + -
176A ILE 2.9 14.2 + - - +
177A HIS* 3.4 13.7 - - - +
178A MET 3.2 0.2 - - - -
179A LEU* 1.3 77.6 - - - +
181A ARG* 1.3 60.9 + - - +
184A LEU* 3.2 37.1 + - + +
186A LYS 5.0 1.4 - - - +
188A VAL* 4.5 9.9 - - + -
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Residues in contact with ARG 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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15A ILE* 3.4 34.1 + - - +
16A SER* 5.3 1.2 + - - -
19A GLU* 3.1 40.0 + - - -
177A HIS 3.0 15.2 + - - +
178A MET* 3.3 15.9 + - - +
180A ALA* 1.3 76.3 - - - +
182A GLU* 1.3 61.4 + - + +
184A LEU 4.3 5.0 - - - +
187A LYS* 3.7 62.5 - - + +
188A VAL* 3.2 35.9 + - + +
190A CYS* 3.9 15.5 - - - -
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Residues in contact with GLU 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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129A ARG* 3.2 40.8 + - - -
178A MET* 3.2 14.4 - - - +
179A LEU* 3.0 11.0 + - + +
181A ARG* 1.3 81.9 - - + +
183A LEU* 1.3 67.1 + - + +
184A LEU 3.6 1.8 - - - +
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Residues in contact with LEU 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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120A ARG* 4.2 6.9 + - - -
121A LEU* 4.0 28.3 - - + +
124A LYS* 4.0 35.7 + - + +
125A THR* 3.4 26.2 - - - +
153A ILE* 5.3 3.1 - - + -
156A VAL* 4.1 23.3 - - + -
179A LEU* 2.9 42.8 + - + +
180A ALA 3.4 0.4 + - - -
182A GLU* 1.3 82.8 - - + +
184A LEU* 1.3 64.9 + - - +
185A PRO* 4.2 1.2 - - - +
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Residues in contact with LEU 184 (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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117A ASN* 5.4 1.6 - - - +
120A ARG* 5.3 2.7 - - - +
121A LEU* 4.6 13.2 - - + -
156A VAL* 3.4 38.4 - - + +
159A ILE* 4.3 13.0 - - + -
160A HIS* 3.7 41.5 - - + +
180A ALA* 3.2 20.1 + - + +
181A ARG 4.3 9.9 - - - +
182A GLU 4.8 1.2 - - - +
183A LEU* 1.3 85.9 + - - +
185A PRO* 1.3 73.5 - - + +
186A LYS* 3.3 18.9 + - + +
187A LYS* 4.4 2.4 + - - +
188A VAL* 5.8 1.6 - - + -
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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