Contacts of the helix formed by residues 183 - 194 (chain A) in PDB entry 3CJD
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 183 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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179A VAL* 3.7 14.4 - - + -
180A PRO* 2.9 16.3 + - + +
182A GLU* 1.3 92.3 - - + +
184A LEU* 1.3 58.7 + - - +
185A LYS 3.4 2.5 - - - -
186A THR* 3.3 28.8 + - - +
187A MSE 2.9 33.3 + - + +
155B LEU* 3.8 35.4 - - + +
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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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98A LEU* 3.7 23.1 - - + -
102A ARG* 3.4 21.3 - - - +
167A ILE* 3.4 34.0 - - + +
168A VAL* 4.9 1.1 - - - +
171A GLY* 3.8 9.9 - - - -
172A LEU* 3.7 22.7 - - + +
179A VAL* 3.8 30.5 - - + +
180A PRO 3.4 5.3 + - - +
181A GLY* 3.4 18.4 + - - +
182A GLU 3.7 0.2 - - - -
183A GLN* 1.3 75.4 - - - +
185A LYS* 1.3 62.2 + - - +
187A MSE 3.5 1.2 + - - +
188A ILE* 3.1 30.5 + - + +
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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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95A HIS* 2.8 60.4 + - + +
98A LEU* 3.7 18.4 - - + -
102A ARG* 6.2 0.4 - - - +
181A GLY 5.0 0.2 + - - -
182A GLU 5.2 2.4 + - - +
183A GLN 3.4 0.4 - - - -
184A LEU* 1.3 77.2 - - - +
186A THR* 1.3 65.4 + - - +
188A ILE 3.3 0.2 + - - -
189A ARG* 3.1 12.3 + - - +
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Residues in contact with THR 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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182A GLU 4.8 3.1 + - - -
183A GLN* 3.3 29.8 + - - +
185A LYS* 1.3 78.8 - - - +
187A MSE 1.3 59.2 + - - +
189A ARG* 3.3 12.9 + - + +
190A LEU* 3.0 44.3 + - + +
155B LEU* 6.0 0.2 - - + -
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Residues in contact with MSE 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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167A ILE* 5.2 2.7 - - + -
179A VAL* 3.6 23.3 - - + -
183A GLN* 2.9 26.0 + - + +
184A LEU* 4.2 2.0 - - - +
186A THR* 1.3 75.0 - - - +
188A ILE* 1.3 59.7 + - - +
190A LEU* 3.5 33.3 + - + +
191A LEU* 3.0 29.1 + - - +
152B GLU 5.3 1.1 - - - +
155B LEU* 3.6 43.1 - - + +
156B MSE 4.0 20.0 - - + +
159B THR* 3.1 44.7 - - + +
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Residues in contact with ILE 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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91A ILE* 4.6 2.2 - - - +
94A SER* 3.3 34.1 - - - +
95A HIS* 4.2 13.9 - - + +
98A LEU* 3.8 31.9 - - + -
164A VAL* 4.5 9.9 - - + -
167A ILE* 4.0 22.2 - - + +
168A VAL* 4.3 15.0 - - + -
184A LEU* 3.1 20.9 + - + +
185A LYS 3.6 3.6 - - - +
187A MSE 1.3 72.9 - - - +
189A ARG* 1.3 66.0 + - - +
191A LEU* 3.4 5.7 + - - +
192A LEU* 3.0 35.6 + - + +
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Residues in contact with ARG 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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88A GLU* 3.2 37.8 + - - -
91A ILE* 3.5 35.9 - - + +
95A HIS* 4.3 10.0 + - - +
185A LYS 3.1 10.2 + - - +
186A THR* 3.4 15.5 - - - +
188A ILE* 1.3 79.2 - - - +
190A LEU* 1.3 60.2 - - + +
193A GLU* 2.8 65.7 + - - +
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Residues in contact with LEU 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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186A THR* 3.0 28.0 + - + +
187A MSE 3.5 41.5 - - + +
188A ILE 3.4 0.2 - - - -
189A ARG* 1.3 79.6 - - + +
191A LEU* 1.3 60.1 + - - +
193A GLU* 3.8 20.4 - - - +
194A GLN* 3.1 30.4 + - - +
156B MSE 4.2 12.8 - - + -
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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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160A LEU* 5.8 0.9 - - + -
163A SER* 4.2 13.2 - - - -
164A VAL* 4.8 4.7 - - + -
167A ILE* 3.4 29.8 - - + -
187A MSE 3.0 18.6 + - - +
188A ILE* 3.6 4.3 - - - +
190A LEU* 1.3 76.2 - - - +
192A LEU* 1.3 77.8 + - + +
194A GLN* 3.5 24.2 + - - +
195A VAL* 4.0 8.1 + - + +
156B MSE 5.2 2.0 - - - +
159B THR* 4.0 8.4 - - + +
160B LEU* 3.9 27.6 - - + -
163B SER* 3.5 11.4 - - - +
191B LEU* 4.5 19.1 - - + -
195B VAL* 5.6 2.5 - - + -
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Residues in contact with LEU 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 ASN* 3.0 23.5 + - - +
90A LEU* 3.8 22.5 - - + +
91A ILE* 3.6 19.3 - - + -
94A SER* 3.2 27.1 - - - +
160A LEU* 4.5 10.1 - - + +
164A VAL* 4.2 8.3 - - + -
188A ILE* 3.0 29.3 + - + +
191A LEU* 1.3 86.7 - - + +
193A GLU* 1.3 60.8 - - - +
194A GLN 3.2 2.0 - - - -
195A VAL* 3.2 26.1 + - + +
203A STE 4.0 19.7 - - + -
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Residues in contact with GLU 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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87A ASN* 3.7 15.1 + - + +
91A ILE* 3.8 13.8 - - + +
189A ARG* 2.8 52.5 + - - +
190A LEU* 3.8 25.8 - - - +
191A LEU 3.4 0.2 - - - -
192A LEU* 1.3 71.6 - - - +
194A GLN* 1.3 60.9 + - + +
195A VAL 3.6 0.2 + - - -
197A ARG 3.3 18.2 - - - +
197B ARG* 5.8 0.3 - - - +
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Residues in contact with GLN 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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190A LEU* 3.1 22.5 + - - +
191A LEU* 3.5 11.4 + - - +
192A LEU 3.2 1.0 - - - -
193A GLU* 1.3 77.3 - - + +
195A VAL* 1.3 63.5 + - - +
196A GLY 3.2 1.0 + - - -
197A ARG* 3.2 14.8 + - - -
145B PHE* 3.5 12.0 - - - -
156B MSE 3.7 26.7 - - - +
160B LEU* 6.1 0.4 - - - +
194B GLN* 3.8 21.8 - - + +
195B VAL* 3.4 9.1 - - + +
196B GLY* 2.7 33.6 + - - -
197B ARG* 3.7 31.0 - - + +
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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