Contacts of the helix formed by residues 200 - 213 (chain A) in PDB entry 3M2K
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 PRO 200 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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81A LEU 5.3 0.2 - - - +
82A GLN* 5.7 2.2 - - + -
198A LYS 5.1 0.2 - - - +
199A LEU* 1.3 90.0 - - + +
201A SER* 1.3 69.9 + - - +
202A GLU* 2.8 6.9 + - + +
203A LYS* 2.9 50.6 + - + +
204A ARG* 3.0 10.2 + - - +
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Residues in contact with SER 201 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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200A PRO* 1.3 72.6 - - - +
202A GLU* 1.3 58.0 + - - +
204A ARG* 3.1 29.5 + - - +
205A GLU* 2.9 42.0 + - - +
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Residues in contact with GLU 202 (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 ILE* 4.1 26.3 - - + +
200A PRO* 2.8 5.0 + - + +
201A SER* 1.3 76.1 + - - +
203A LYS* 1.3 66.1 + - + +
205A GLU* 3.4 28.2 - - - +
206A LEU* 3.8 11.6 + - - +
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Residues in contact with LYS 203 (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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81A LEU* 3.3 55.2 + - + +
82A GLN 4.5 3.8 + - - -
86A LYS 2.8 31.2 + - - -
87A SER* 4.0 6.3 - - - +
88A ILE* 4.2 24.7 - - + -
199A LEU* 4.5 2.2 - - + -
200A PRO* 2.9 39.6 + - + +
202A GLU* 1.3 78.3 - - - +
204A ARG* 1.3 65.9 - - - +
205A GLU 3.2 0.2 - - - -
206A LEU* 3.2 15.6 + - - +
207A LEU 3.3 9.0 + - - -
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Residues in contact with ARG 204 (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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193A PHE 3.9 9.2 + - - +
194A ALA* 3.2 36.3 - - - +
195A LEU* 4.5 4.9 + - - +
196A GLU 3.5 23.9 + - - -
197A ASP* 4.3 11.1 + - - -
199A LEU* 2.5 40.3 + - + -
200A PRO* 3.0 8.1 + - - +
201A SER* 3.1 35.8 + - - +
203A LYS* 1.3 79.6 - - - +
205A GLU* 1.4 66.2 + - - +
207A LEU* 3.2 7.0 - - - +
208A ILE* 3.0 27.1 + - + +
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Residues in contact with GLU 205 (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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201A SER* 2.9 29.6 + - - +
202A GLU* 3.4 23.1 - - - +
204A ARG* 1.4 76.3 - - - +
206A LEU* 1.3 54.3 + - + +
208A ILE* 3.5 8.6 + - - +
209A ASP* 2.7 36.3 + - - +
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Residues in contact with LEU 206 (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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81A LEU* 5.1 4.7 - - + -
88A ILE* 3.7 34.3 - - + -
91A LEU* 4.8 7.4 - - + -
120A LYS* 4.5 24.5 - - - +
202A GLU 4.0 8.7 - - - +
203A LYS* 3.2 9.1 + - - +
205A GLU* 1.3 77.7 - - + +
207A LEU* 1.3 71.6 + - - +
209A ASP* 3.4 11.2 - - + +
210A TRP* 2.7 55.3 + - + +
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Residues in contact with LEU 207 (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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74A ALA 4.7 7.6 - - - +
77A VAL* 3.4 28.7 - - + -
78A GLY* 4.5 7.2 - - - -
81A LEU* 4.4 4.4 - - + +
127A LEU* 4.0 13.7 - - + -
190A LEU* 5.7 2.5 - - + -
193A PHE* 4.4 15.3 - - + -
194A ALA* 4.8 13.5 - - + +
199A LEU* 4.3 22.7 - - + -
203A LYS 3.3 7.6 + - - +
204A ARG* 3.2 10.5 - - - +
206A LEU* 1.3 71.4 - - - +
208A ILE* 1.3 82.4 - - - +
210A TRP* 2.6 14.7 + - + +
211A MET* 3.0 24.9 + - - -
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Residues in contact with ILE 208 (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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194A ALA* 3.8 30.7 - - + +
195A LEU* 5.1 1.3 - - + -
204A ARG* 3.0 17.8 + - + +
205A GLU* 3.5 9.4 - - - +
207A LEU* 1.3 95.3 - - - +
209A ASP* 1.3 96.7 - - + +
211A MET* 2.2 23.8 + - - +
212A LYS* 3.3 29.3 + - + +
232A ALA* 4.9 3.4 - - + -
249A ILE* 5.2 0.7 - - + -
251A TRP* 4.0 29.8 - - + -
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Residues in contact with ASP 209 (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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205A GLU 2.7 16.2 + - - +
206A LEU* 3.4 14.2 - - + +
208A ILE* 1.3 88.5 - - + +
210A TRP* 1.3 69.0 + - - +
211A MET 2.9 0.9 + - - -
212A LYS* 3.2 15.3 + - - +
213A ARG* 2.8 64.9 + - - +
120B LYS* 4.5 15.2 + - - -
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Residues in contact with TRP 210 (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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77A VAL* 4.3 11.2 - - + -
81A LEU* 4.4 8.5 - - + -
91A LEU* 4.5 19.1 - - + -
120A LYS* 3.8 27.9 - - + +
123A ALA* 3.2 30.3 - - + -
124A ASP* 2.9 42.1 + - - +
127A LEU* 3.4 35.1 - - + +
128A ARG* 3.4 26.8 + - + +
206A LEU* 2.7 49.8 + - + +
207A LEU* 2.6 10.7 + - + +
208A ILE 2.3 5.9 + - - -
209A ASP* 1.3 81.8 + - - +
211A MET* 1.3 59.3 + - - +
213A ARG* 3.4 7.7 + - - +
214A ASN* 3.5 3.8 + - - -
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Residues in contact with MET 211 (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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74A ALA* 4.3 22.4 - - + -
127A LEU* 5.0 14.6 - - + +
190A LEU* 3.7 40.6 - - + -
194A ALA* 6.1 1.1 - - - -
207A LEU* 3.0 25.4 + - + +
208A ILE* 2.2 25.3 + - - +
210A TRP* 1.3 65.9 - - - +
212A LYS* 1.3 53.6 + - - +
214A ASN* 3.4 3.7 + - - +
222A ARG* 2.7 31.0 + - - -
232A ALA* 3.3 24.9 - - + +
233A ASP* 3.2 22.1 + - - +
234A LYS* 3.9 21.8 - - + +
247A ILE* 4.4 2.0 - - + +
249A ILE* 5.2 4.3 - - + -
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Residues in contact with LYS 212 (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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208A ILE* 3.3 31.5 + - + +
209A ASP* 3.2 17.4 + - - +
211A MET* 1.3 75.7 - - - +
213A ARG* 1.3 69.7 + - + +
214A ASN 2.7 8.5 + - - +
222A ARG* 3.1 19.1 + - - +
230A GLU* 2.8 34.8 + - + +
231A VAL 4.0 13.7 - - - +
232A ALA* 3.5 11.3 - - + +
251A TRP* 4.9 1.3 - - + -
120B LYS* 5.7 6.1 - - - +
213B ARG* 4.3 5.4 + - - -
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Residues in contact with ARG 213 (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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124A ASP* 3.7 20.2 + - - -
128A ARG* 2.9 42.9 + - - +
209A ASP* 2.8 48.4 + - - +
210A TRP* 3.7 5.7 - - - -
211A MET 3.3 0.2 - - - -
212A LYS* 1.3 85.1 - - + +
214A ASN* 1.3 63.9 + - - +
120B LYS* 5.8 4.8 - - - +
206B LEU* 6.3 4.0 - - - -
209B ASP* 3.4 24.0 + - - +
210B TRP* 5.6 2.9 - - - +
213B ARG* 3.3 39.9 - - - +
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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