Contacts of the helix formed by residues 211 - 216 (chain A) in PDB entry 1SEJ
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 LYS 211 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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200A VAL* 3.9 30.9 - - - +
203A LEU* 4.2 9.2 - - + +
204A GLY* 4.1 20.2 - - - +
207A PHE* 4.1 6.8 - - + +
208A GLY 3.1 10.5 + - - +
209A ILE 3.8 2.9 - - - +
210A ARG* 1.3 78.0 - - - +
212A MET* 1.3 66.2 + - - +
213A GLY* 4.1 12.7 - - - +
214A ASN* 2.8 33.4 + - - +
215A ARG 3.8 1.6 + - - -
158B TYR* 4.4 0.4 + - - -
161B GLN* 3.6 13.4 + - - +
163B PHE* 3.8 23.6 - - + -
234B GLU* 2.6 42.4 + - - -
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Residues in contact with MET 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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210A ARG 3.3 5.9 + - - -
211A LYS* 1.3 70.1 - - - +
213A GLY* 1.3 54.8 + - - +
215A ARG* 2.7 59.9 + - - +
216A HIS* 3.3 17.8 + - + +
161B GLN* 3.0 12.6 + - - +
236B TYR* 3.3 34.8 - - + +
271B ARG* 3.6 25.1 - - + -
272B PHE 4.7 2.5 - - - -
273B ASP* 3.4 33.4 - - + -
455B GLU* 3.2 32.5 - - + +
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Residues in contact with GLY 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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211A LYS* 3.0 15.7 + - - +
212A MET* 1.3 78.4 - - - +
214A ASN* 1.3 58.0 + - - +
216A HIS* 2.9 34.1 + - - +
217A LYS* 3.5 2.6 + - - +
161B GLN* 4.1 4.0 + - - -
236B TYR* 4.2 6.4 + - - -
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Residues in contact with ASN 214 (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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204A GLY* 3.9 31.5 + - - -
208A GLY* 3.2 33.5 + - - +
209A ILE* 4.6 3.4 - - - -
211A LYS* 2.8 20.7 + - - +
213A GLY* 1.3 72.4 - - - -
215A ARG* 1.3 58.1 + - - +
216A HIS 3.2 0.2 - - - -
217A LYS* 3.2 49.2 + - - +
250A ASN* 4.4 1.4 + - - -
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Residues in contact with ARG 215 (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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209A ILE* 2.7 37.1 + - + +
210A ARG 3.4 22.2 + - - -
212A MET* 2.7 36.7 + - - +
214A ASN* 1.3 72.8 - - - +
216A HIS* 1.3 71.1 + - + +
217A LYS 3.6 1.1 - - - -
250A ASN* 3.3 18.5 + - - +
273B ASP* 3.0 22.8 + - - -
275B ARG* 3.4 47.1 - - - +
455B GLU* 2.8 47.8 + - - +
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Residues in contact with HIS 216 (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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212A MET* 3.4 30.7 - - + +
213A GLY* 2.9 14.9 + - - +
215A ARG* 1.3 86.9 + - + +
217A LYS* 1.3 66.0 + - - +
218A PHE* 3.5 2.4 + - - +
246A ARG* 6.3 0.9 - - - -
250A ASN* 3.6 4.7 - - - +
266A PHE 5.5 3.1 - - - -
268A GLN* 4.8 6.5 + - - -
236B TYR* 5.4 0.7 - - - -
271B ARG* 3.6 31.8 + - - -
455B GLU* 2.8 31.7 + - - -
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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