Contacts of the helix formed by residues 171 - 186 (chain A) in PDB entry 2B4J
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 HIS 171 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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166A ARG* 3.9 2.1 + - - -
169A ALA* 3.8 3.1 - - - +
170A GLU* 1.3 96.9 - - + +
172A LEU* 1.3 65.2 + - - +
173A LYS* 4.2 23.5 - - + +
174A THR* 3.1 13.6 + - - +
175A ALA 3.3 8.3 + - - -
404A GOL 3.1 42.7 - - - -
95B GLN* 6.0 2.7 - - + -
366C ASP* 2.8 36.1 + - - +
367C ASN* 5.5 2.9 - - + -
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Residues in contact with LEU 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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68A LEU* 3.4 39.9 - - + +
69A GLU* 3.8 33.7 - - + +
71A LYS* 3.8 26.7 - - + -
73A ILE* 4.5 3.8 - - + -
88A VAL* 4.2 10.8 - - + -
162A ILE* 4.0 24.7 - - + -
166A ARG* 3.3 12.7 - - - +
171A HIS* 1.3 70.9 - - - +
173A LYS* 1.3 64.0 + - - +
175A ALA* 3.0 3.8 + - + +
176A VAL* 2.9 28.2 + - + +
404A GOL 3.1 13.6 + - - +
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Residues in contact with LYS 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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71A LYS* 5.7 0.6 - - - +
88A VAL* 3.6 29.4 - - + +
171A HIS* 3.2 19.0 - - + +
172A LEU* 1.3 77.8 - - - +
174A THR* 1.3 67.5 + - - +
176A VAL* 3.6 3.3 + - - +
177A GLN* 3.5 25.8 + - - +
404A GOL 5.1 6.5 - - - +
95B GLN* 5.2 12.6 - - - +
96B GLU* 4.4 14.5 + - - -
99B TYR* 3.7 47.3 - - + +
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Residues in contact with THR 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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169A ALA* 3.7 14.4 - - + -
171A HIS* 3.1 4.5 + - - +
173A LYS* 1.3 83.3 - - - +
175A ALA* 1.3 60.4 + - - +
177A GLN* 3.2 4.6 + - - +
178A MET* 3.0 28.1 + - + +
95B GLN* 4.8 6.1 + - - +
99B TYR* 4.8 8.1 - - - -
102B LEU* 3.7 26.0 - - + -
365C ILE* 4.0 19.7 - - + -
366C ASP* 2.9 36.3 + - + +
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Residues in contact with ALA 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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162A ILE* 4.2 11.7 - - + +
165A VAL* 3.9 12.5 - - + +
166A ARG* 3.9 29.4 - - - -
169A ALA* 3.9 13.3 - - + +
171A HIS 3.3 6.9 + - - +
172A LEU* 3.0 9.4 + - - +
174A THR* 1.3 74.9 - - - +
176A VAL* 1.3 61.0 + - - +
178A MET* 3.3 10.2 + - - +
179A ALA* 2.9 29.8 + - - +
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Residues in contact with VAL 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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73A ILE* 3.8 22.9 - - + -
86A ALA* 3.9 38.6 - - + +
87A GLU* 4.2 5.6 - - - +
88A VAL* 3.9 11.7 - - + -
158A LEU* 4.6 2.0 - - + +
162A ILE* 3.7 28.3 - - + -
172A LEU* 2.9 24.0 + - + +
173A LYS 3.8 6.1 - - - +
175A ALA* 1.3 76.1 - - - +
177A GLN* 1.3 62.4 + - - +
179A ALA* 3.1 3.8 + - - +
180A VAL* 3.0 26.9 + - + +
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Residues in contact with GLN 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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86A ALA 2.7 28.3 + - - +
87A GLU* 3.6 24.0 - - - +
88A VAL 4.8 0.2 - - - +
173A LYS 3.5 11.2 + - - +
174A THR 3.2 7.2 + - - +
176A VAL* 1.3 76.7 - - - +
178A MET* 1.3 67.2 + - - +
180A VAL* 3.4 13.5 + - - +
181A PHE* 3.1 23.9 + - - +
99B TYR* 3.8 15.6 + - + -
102B LEU* 4.2 28.5 - - + +
103B LYS* 3.5 33.2 - - + +
106B GLY* 5.5 0.7 - - - -
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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
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165A VAL* 4.0 12.8 - - + +
168A GLN* 3.6 28.3 - - + +
169A ALA* 4.2 13.2 - - + -
174A THR* 3.0 20.2 + - + +
175A ALA* 3.5 10.3 - - - +
177A GLN* 1.3 79.8 - - - +
179A ALA* 1.3 56.7 + - - +
181A PHE* 3.4 2.9 - - - +
182A ILE* 3.1 34.2 + - - +
102B LEU* 5.0 4.2 - - + +
132B TRP* 3.4 55.9 - - + +
365C ILE* 3.4 36.6 - - + -
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Residues in contact with ALA 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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158A LEU* 3.8 10.5 - - + -
161A ILE* 3.6 33.5 - - + +
162A ILE* 3.7 24.5 - - + +
165A VAL* 4.5 0.9 - - + +
175A ALA 2.9 16.5 + - - +
176A VAL 3.1 4.4 + - - +
178A MET* 1.3 76.1 - - - +
180A VAL* 1.3 59.1 + - - +
182A ILE* 3.4 2.0 + - - +
183A HIS* 2.9 30.1 + - - +
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Residues in contact with VAL 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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84A ILE* 3.5 33.4 - - + +
85A GLU* 4.3 5.8 - - + -
86A ALA* 3.8 38.4 - - + +
158A LEU* 4.3 7.4 - - + -
176A VAL 3.0 20.4 + - - +
177A GLN* 3.4 12.8 + - - +
179A ALA* 1.3 75.5 - - - +
181A PHE* 1.3 57.2 + - - +
183A HIS* 3.3 5.9 + - - +
184A ASN* 2.9 37.6 + - - +
103B LYS 6.0 1.3 - - - +
106B GLY* 4.8 8.1 - - - +
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Residues in contact with PHE 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 GLN 3.1 13.3 + - - +
178A MET 3.4 8.5 - - - +
180A VAL* 1.3 75.4 - - - +
182A ILE* 1.3 69.6 + - + +
184A ASN 3.8 0.2 - - - -
185A LYS* 3.0 53.1 + - + +
102B LEU* 5.0 3.6 - - + +
105B ALA* 3.5 42.4 - - + -
106B GLY* 3.7 13.4 - - - -
132B TRP* 3.5 31.4 - + + -
133B ALA* 3.5 33.2 - - + -
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Residues in contact with ILE 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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161A ILE* 3.8 18.4 - - + -
164A GLN* 5.5 2.5 - - - +
165A VAL* 3.3 34.3 - - + -
178A MET 3.1 16.9 + - - +
179A ALA 3.8 3.8 - - - +
180A VAL 3.4 0.2 - - - -
181A PHE* 1.3 82.7 - - + +
183A HIS* 1.3 64.1 + - - +
185A LYS* 4.4 1.7 - - - +
186A LYS* 3.0 42.6 + - + +
132B TRP* 4.1 18.4 - - + -
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Residues in contact with HIS 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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82A GLY* 2.8 30.1 - - - -
84A ILE* 3.8 23.3 - - + +
154A MET* 3.6 26.2 - - - +
157A GLU* 4.1 25.7 - - + +
158A LEU* 5.8 0.7 - - + -
161A ILE* 3.9 13.0 - - + +
179A ALA 2.9 17.8 + - - +
180A VAL 3.5 4.3 - - - +
182A ILE* 1.3 80.4 - - - +
184A ASN* 1.3 73.5 + - - +
185A LYS 3.4 0.2 + - - -
186A LYS* 3.5 21.9 + - - +
196A ALA* 4.3 8.9 - - + +
199A ARG* 5.9 0.4 - - - -
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Residues in contact with ASN 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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83A TYR* 3.3 23.1 + - + -
84A ILE* 2.8 44.6 + - - -
180A VAL* 2.9 26.8 + - - +
181A PHE 4.1 1.6 - - - +
183A HIS* 1.3 83.7 + - - +
185A LYS* 1.3 61.2 + - + +
195A SER* 3.4 10.5 + - - -
196A ALA* 3.6 2.3 + - - -
197A GLY* 2.9 33.0 + - - +
106B GLY 3.1 26.9 + - - +
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Residues in contact with LYS 185 (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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181A PHE* 3.0 52.3 + - + +
182A ILE* 4.4 1.8 - - - +
184A ASN* 1.3 79.3 - - + +
186A LYS* 1.3 67.4 + - - +
195A SER* 3.5 11.3 - - - -
197A GLY* 6.0 4.1 - - - -
105B ALA 2.9 29.0 + - - -
106B GLY 4.1 10.7 + - - -
107B ARG 4.6 0.8 - - - -
108B TRP* 3.0 26.3 + - - +
109B PRO* 4.0 8.5 - - - +
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Residues in contact with LYS 186 (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 GLU* 4.4 10.0 + - - -
161A ILE* 4.2 21.2 - - - +
182A ILE* 3.0 30.4 + - + +
183A HIS* 3.5 16.0 + - - +
185A LYS* 1.3 80.8 - - - +
195A SER* 3.4 25.0 + - - -
196A ALA 4.3 2.6 + - - -
199A ARG* 5.5 0.7 + - - -
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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