Contacts of the helix formed by residues 182 - 197 (chain A) in PDB entry 3CEI
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 ASN 182 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78A ASP* 3.0 28.8 + - - +
79A CYS 2.8 15.3 + - - +
80A LEU 3.8 6.4 + - - +
81A SER* 3.8 18.9 - - - -
85A THR* 2.7 29.5 + - - +
180A HIS 3.3 0.8 + - - -
181A ILE* 1.3 71.1 - - - +
183A TRP* 1.3 62.6 + - - +
184A HIS* 3.4 7.4 - - - +
185A PHE* 2.9 29.9 + - - +
186A VAL* 3.0 12.5 + - - +
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Residues in contact with TRP 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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84A ALA* 4.5 7.7 - - + +
85A THR* 3.0 28.9 + - - +
86A ALA 3.4 10.5 - - - +
87A LEU* 3.3 38.9 - - + +
91A LEU* 3.9 8.2 - - + +
95A LEU* 4.2 18.8 - - + -
102A LEU* 6.4 0.4 - - + -
105A PHE* 4.1 15.9 - + - -
153A LEU* 4.5 3.8 - - + -
178A TYR* 3.6 37.1 + + - -
181A ILE* 3.0 52.8 + - + +
182A ASN* 1.3 72.6 - - - +
184A HIS* 1.3 51.9 + - - +
186A VAL* 3.5 16.3 - - + +
187A SER* 2.7 38.8 + - - -
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Residues in contact with HIS 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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85A THR* 2.9 27.3 + - + +
86A ALA* 3.2 13.1 + - - +
182A ASN* 3.4 6.1 - - - +
183A TRP* 1.3 76.2 - - - +
185A PHE* 1.3 63.5 + - + +
187A SER* 3.4 7.0 + - - -
188A GLN* 3.2 39.7 + - + +
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Residues in contact with PHE 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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75A PHE* 3.8 20.2 - + - -
78A ASP* 3.4 40.6 - - + -
79A CYS* 4.0 15.7 - - - -
152A LEU 4.9 0.2 - - - -
182A ASN* 2.9 28.7 + - - +
184A HIS* 1.3 78.6 - - - +
186A VAL* 1.3 67.9 + - - +
187A SER 3.1 1.6 - - - -
188A GLN* 3.1 25.3 + - - +
189A CYS* 3.0 46.7 + - - -
204A TYR* 3.6 31.9 - + - -
208A LEU* 6.1 1.8 - - + -
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Residues in contact with VAL 186 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A CYS* 5.2 0.7 - - + -
91A LEU* 3.7 22.0 - - + -
95A LEU* 6.0 0.2 - - + -
124A ALA* 6.2 0.2 - - + -
152A LEU* 3.3 40.2 - - + +
153A LEU* 3.9 26.7 - - + -
181A ILE* 4.0 11.4 - - + -
182A ASN 3.0 13.9 + - - +
183A TRP* 3.0 17.9 + - + +
185A PHE* 1.3 80.7 - - + +
187A SER* 1.3 61.7 + - - +
189A CYS* 3.4 2.8 + - - +
190A TYR* 3.1 21.1 + - - +
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Residues in contact with SER 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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86A ALA 4.1 0.6 + - - -
87A LEU* 3.7 1.2 - - - -
88A SER* 2.9 47.1 + - - -
90A GLU* 5.4 0.7 - - - +
91A LEU* 3.4 13.5 - - - +
183A TRP 2.7 22.1 + - - -
184A HIS* 3.5 8.7 - - - -
186A VAL* 1.3 71.2 - - - +
188A GLN* 1.3 64.8 + - - +
190A TYR* 3.2 5.5 + - - +
191A GLU* 2.9 25.6 + - - +
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Residues in contact with GLN 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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184A HIS* 3.2 34.3 + - + +
185A PHE* 3.1 27.9 + - + +
187A SER* 1.3 77.4 - - - +
189A CYS* 1.3 63.8 + - - +
191A GLU* 3.3 7.1 + - - +
192A TRP* 3.0 68.2 + - + +
208A LEU* 5.1 7.5 - - - +
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Residues in contact with CYS 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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75A PHE* 3.7 17.5 - - - -
150A VAL* 4.5 3.9 - - + +
151A PRO 3.7 15.3 - - - +
152A LEU* 3.6 9.9 - - + +
185A PHE* 3.0 50.6 + - - -
186A VAL 3.6 8.1 - - - +
187A SER 3.3 0.2 - - - -
188A GLN* 1.3 80.1 - - - +
190A TYR* 1.3 57.6 + - - +
192A TRP* 3.6 6.6 + - - +
193A ALA* 2.9 30.1 + - - +
200A SER* 4.9 0.7 + - - -
204A TYR* 5.7 2.2 - - - -
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Residues in contact with TYR 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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88A SER* 5.1 0.2 - - - -
90A GLU* 3.9 23.7 + - - -
91A LEU* 3.9 27.4 - - + -
94A ALA* 3.1 20.8 - - + +
97A LYS* 6.0 0.5 - - - -
126A TYR* 3.8 26.7 - + - -
131A GLN 5.6 0.9 + - - -
133A ILE* 4.0 12.3 - - + -
152A LEU* 3.5 26.2 - - + +
186A VAL 3.1 13.5 + - - +
187A SER 3.5 7.6 - - - +
188A GLN 3.2 0.2 - - - -
189A CYS* 1.3 74.3 - - - +
191A GLU* 1.3 69.1 + - - +
193A ALA* 2.9 12.9 + - - +
194A LYS* 3.1 54.0 + - + +
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Residues in contact with GLU 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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90A GLU* 3.9 31.7 - - - +
187A SER 2.9 16.8 + - - +
188A GLN* 3.7 6.2 - - - +
190A TYR* 1.3 76.9 - - - +
192A TRP* 1.3 80.9 + - + +
194A LYS* 3.2 7.3 + - - +
195A LYS* 3.1 61.7 + - - +
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Residues in contact with TRP 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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188A GLN* 3.0 53.4 + - + +
189A CYS* 4.2 4.3 - - - +
191A GLU* 1.3 101.8 + - + +
193A ALA* 1.3 60.0 + - - +
194A LYS 3.2 0.2 - - - -
195A LYS* 3.7 11.7 - - + +
196A GLU* 2.8 28.8 + - + +
197A GLY 3.4 0.5 + - - -
200A SER* 3.3 30.6 - - - -
203A TYR* 4.0 35.0 - + - -
204A TYR* 5.9 7.0 - + + -
208A LEU* 4.8 12.6 - - + -
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Residues in contact with ALA 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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126A TYR* 4.0 22.2 - - + -
128A LEU* 3.8 8.7 - - - +
150A VAL* 3.7 25.8 - - + -
152A LEU* 4.3 1.1 - - + -
189A CYS 2.9 19.9 + - - +
190A TYR* 2.9 7.5 + - - +
192A TRP* 1.3 76.7 - - - +
194A LYS* 1.3 59.8 - - - +
197A GLY* 2.8 30.6 + - - -
200A SER* 3.8 8.3 - - - -
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Residues in contact with LYS 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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90A GLU* 3.0 33.1 + - - +
126A TYR* 3.8 28.3 - - + +
128A LEU* 5.6 0.6 - - - +
190A TYR* 3.1 52.8 + - + +
191A GLU* 3.5 9.0 - - - +
193A ALA* 1.3 78.9 - - - +
195A LYS* 1.3 62.4 + - + +
197A GLY 4.6 0.7 + - - -
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Residues in contact with LYS 195 (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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191A GLU* 3.1 50.3 + - + +
192A TRP* 4.2 9.0 - - + +
193A ALA 3.4 0.2 - - - -
194A LYS* 1.3 82.9 - - + +
196A GLU* 1.3 77.9 + - + +
197A GLY 3.6 0.2 - - - -
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Residues in contact with GLU 196 (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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192A TRP* 2.8 19.0 + - + +
195A LYS* 1.3 91.4 - - + +
197A GLY* 1.3 65.6 - - - +
198A LEU 3.5 0.2 + - - -
199A GLY* 2.9 17.1 + - - -
200A SER* 3.7 19.1 - - - +
203A TYR* 6.5 0.7 - - + -
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Residues in contact with GLY 197 (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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128A LEU* 3.8 15.9 - - - -
150A VAL* 3.9 8.1 - - - +
192A TRP 3.4 0.8 + - - +
193A ALA 2.8 23.5 + - - +
194A LYS 4.5 0.4 - - - -
195A LYS 3.6 1.2 - - - -
196A GLU* 1.3 76.7 - - - +
198A LEU* 1.3 55.9 - - - -
199A GLY 2.8 4.3 + - - -
200A SER* 2.6 29.6 + - - -
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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