Contacts of the helix formed by residues 179 - 194 (chain A) in PDB entry 3JCA
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 THR 179 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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177A TYR* 3.5 10.6 - - - +
178A TYR* 1.3 98.0 - - + +
180A PRO* 1.3 71.5 - - + +
181A HIS* 3.2 10.9 + - - +
182A HIS* 2.7 37.6 + - - +
183A LEU* 3.2 5.4 + - - +
94B ARG* 5.6 2.9 - - - +
104B GLN* 2.6 31.8 + - + +
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Residues in contact with PRO 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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72A PHE* 3.5 54.5 - - + -
75A LEU* 3.7 27.4 - - + -
93A ALA* 5.4 2.0 - - + +
168A LEU* 5.8 0.2 - - - +
178A TYR 4.8 0.7 - - - +
179A THR* 1.3 89.3 - - + +
181A HIS* 1.3 61.5 + - + +
183A LEU* 3.5 5.2 + - + +
184A LEU* 2.9 27.0 + - - +
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Residues in contact with HIS 181 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A LEU* 4.3 12.0 - - + +
92A THR* 5.6 3.4 - - + +
93A ALA* 3.1 46.8 + - + +
94A ARG* 6.2 2.0 - - - -
179A THR* 3.1 11.5 + - + +
180A PRO* 1.3 79.9 - - + +
182A HIS* 1.3 56.3 + - - +
184A LEU* 4.1 9.0 - - + -
185A ALA* 2.8 36.4 + - - +
104B GLN* 3.7 11.4 + - - +
108B GLN* 4.9 10.3 + - - +
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Residues in contact with HIS 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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176A LYS 5.0 2.0 - - - -
177A TYR* 3.7 20.5 - + + -
178A TYR* 2.9 31.1 + - + +
179A THR* 2.7 30.2 + - - +
181A HIS* 1.3 73.4 - - - +
183A LEU* 1.3 62.6 + - - +
185A ALA* 3.9 3.1 - - - +
186A HIS* 3.0 21.4 + - + +
100B LYS* 6.1 2.9 - - + -
103B LEU* 4.9 14.3 + - + +
104B GLN* 3.4 17.4 - - - +
107B ALA* 3.8 22.7 - - + +
135B PHE* 5.1 18.5 - + - -
139B TRP* 5.6 6.7 - - - -
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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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71A GLU* 4.5 3.4 - - - +
72A PHE* 3.8 21.5 - - + -
168A LEU* 3.6 34.3 - - + +
171A LEU* 3.5 32.3 - - + -
172A GLN* 3.7 22.9 - - + +
177A TYR* 3.6 34.6 - - + -
179A THR 3.2 7.2 + - - +
180A PRO* 3.6 8.5 - - + +
182A HIS* 1.3 78.9 - - - +
184A LEU* 1.3 63.7 + - - +
186A HIS* 3.1 5.5 + - - +
187A ALA* 3.0 19.1 + - - +
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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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72A PHE* 6.4 0.7 - - + -
78A VAL* 4.9 6.1 - - + -
91A ALA* 3.5 42.2 - - + +
92A THR* 4.1 0.4 - - - -
93A ALA* 3.6 33.2 - - + +
164A ILE* 4.8 10.8 - - + -
168A LEU* 4.1 22.4 - - + -
180A PRO 2.9 17.7 + - - +
181A HIS* 3.8 9.9 - - + +
183A LEU* 1.3 75.5 - - - +
185A ALA* 1.3 57.9 + - - +
187A ALA* 3.0 5.6 + - + +
188A LEU* 2.8 35.7 + - + +
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Residues in contact with ALA 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 HIS 2.8 22.4 + - - +
182A HIS* 3.9 3.4 - - - +
184A LEU* 1.3 72.2 - - - +
186A HIS* 1.3 62.8 + - - +
188A LEU* 3.2 12.3 + - - +
189A PHE* 2.9 24.8 + - - +
107B ALA* 3.8 29.4 - - + +
108B GLN* 4.2 15.5 - - + +
111B ALA* 3.8 7.5 - - + +
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Residues in contact with HIS 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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171A LEU* 3.6 20.4 - - + +
174A ALA* 6.5 0.2 - - + -
177A TYR* 3.3 30.3 + - + -
182A HIS* 3.0 17.1 + - + +
183A LEU 3.1 9.8 + - - +
185A ALA* 1.3 77.4 - - - +
187A ALA* 1.3 61.7 + - - +
189A PHE* 3.3 8.1 + + - +
190A VAL* 3.0 24.8 + - + +
107B ALA* 5.2 4.0 - - + +
139B TRP* 5.8 6.7 - + - -
11E LEU* 3.5 23.5 + - + -
12E HIS* 2.8 34.4 + + - -
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Residues in contact with ALA 187 (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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164A ILE* 5.2 2.2 - - + +
167A GLN* 3.7 21.5 - - + -
168A LEU* 3.8 21.1 - - + -
171A LEU* 3.5 12.0 - - + +
183A LEU 3.0 12.5 + - - +
184A LEU* 3.0 11.6 + - + +
186A HIS* 1.3 76.4 - - - +
188A LEU* 1.3 56.9 + - + +
190A VAL* 3.1 3.4 + - - +
191A LEU* 2.8 39.9 + - + +
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Residues in contact with LEU 188 (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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89A THR* 4.1 13.9 - - - +
90A PHE* 3.8 29.6 - - + +
91A ALA* 3.5 46.4 - - + +
112A TYR* 3.7 21.8 + - + +
164A ILE* 5.6 2.9 - - + -
184A LEU* 2.8 29.5 + - + +
185A ALA* 3.7 10.5 - - + +
187A ALA* 1.3 74.0 - - - +
189A PHE* 1.3 63.9 + - - +
191A LEU* 3.4 10.4 + - + +
192A ASN* 3.1 22.0 + - - +
111B ALA* 4.1 6.3 - - + -
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Residues in contact with PHE 189 (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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185A ALA 2.9 13.2 + - - +
186A HIS* 3.4 12.3 - + - +
188A LEU* 1.3 77.0 - - - +
190A VAL* 1.3 60.6 + - + +
193A HIS* 2.8 56.7 + + + +
194A VAL* 3.3 26.8 + - + -
107B ALA 5.2 0.2 - - - +
110B PHE* 3.2 33.2 - + + -
111B ALA* 4.1 11.6 - - - +
114B GLY* 3.9 7.2 - - - -
115B ILE* 3.4 43.7 - - + -
12E HIS* 3.7 23.3 - + - -
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Residues in contact with VAL 190 (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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167A GLN* 3.6 30.1 - - - +
171A LEU* 4.9 0.4 - - + -
186A HIS* 3.0 30.4 + - + +
187A ALA 3.5 6.3 - - - +
189A PHE* 1.3 77.9 - - + +
191A LEU* 1.3 63.1 + - - +
194A VAL* 3.0 24.3 + - + -
195A ASN* 2.8 35.2 + - + +
12E HIS* 3.5 34.5 - - + +
13E HIS 4.6 5.6 - - - +
14E GLN* 5.4 0.2 - - - -
15E ASN 6.0 0.2 - - - +
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Residues in contact with LEU 191 (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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89A THR* 4.0 21.5 - - + +
160A THR* 5.9 0.7 - - + -
163A ASN* 4.4 18.2 - - + +
164A ILE* 3.8 33.7 - - + -
167A GLN* 3.8 28.5 - - + +
187A ALA* 2.8 32.7 + - + +
188A LEU* 3.8 11.0 - - + +
190A VAL* 1.3 73.8 - - - +
192A ASN* 1.3 63.4 + - - +
195A ASN* 3.8 28.3 + - - +
203A ALA* 4.0 8.5 - - - +
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Residues in contact with ASN 192 (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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87A HIS 4.3 0.7 - - - +
88A PHE* 3.5 28.3 - - + -
89A THR* 2.7 53.1 + - - +
112A TYR* 2.9 18.4 + - - +
188A LEU 3.1 10.9 + - - +
191A LEU* 1.3 80.9 - - - +
193A HIS* 1.3 68.0 + - + +
194A VAL 3.8 0.4 - - - -
195A ASN 5.0 0.4 - - - -
202A THR* 3.4 10.4 - - - -
203A ALA* 3.5 17.2 + - - +
204A ALA* 3.0 26.7 + - + +
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Residues in contact with HIS 193 (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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88A PHE* 5.2 4.2 - + - -
112A TYR* 4.7 0.6 + - - -
188A LEU 4.6 0.2 - - - -
189A PHE* 2.8 43.1 + + + +
192A ASN* 1.3 82.6 - - + +
194A VAL* 1.3 62.8 + - - +
202A THR* 3.8 17.2 + - - +
204A ALA* 3.5 26.2 - - + +
208A TRP* 5.4 4.6 - + - -
59B ARG* 6.2 1.4 - - - -
110B PHE 3.6 18.3 + - - -
111B ALA 2.9 24.5 + - - -
112B TYR 4.5 4.9 + - - -
113B MET 4.5 15.9 + - - -
114B GLY* 4.6 4.8 - - - -
208B TRP* 6.2 2.2 - + - -
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Residues in contact with VAL 194 (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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189A PHE* 3.3 39.3 - - + -
190A VAL* 3.0 26.6 + - + +
193A HIS* 1.3 79.2 - - - +
195A ASN* 1.3 66.0 + - - +
196A MET* 3.2 6.2 + - - +
202A THR* 4.9 2.0 - - - +
12E HIS* 4.3 13.5 - - + -
14E GLN* 3.3 46.5 + - + +
18E ALA* 3.2 17.3 - - - +
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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