Contacts of the helix formed by residues 214 - 219 (chain A) in PDB entry 1U2X
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 PHE 214 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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96A LEU* 4.0 25.8 - - + -
97A VAL* 3.8 14.6 - - - +
98A ASN 4.2 2.5 - - - -
99A GLU* 3.6 47.1 - - + +
102A ASN* 3.6 12.6 - - - -
179A LEU 3.4 24.5 - - - -
212A ALA* 3.9 19.4 - - + -
213A ARG* 1.3 76.3 - - - +
215A GLU* 1.3 67.5 + - - +
216A SER* 3.3 28.4 + - - -
217A ILE* 3.3 39.9 + - + +
218A SER* 3.8 4.0 + - - -
249A ARG* 3.3 8.5 - - - +
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Residues in contact with GLU 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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214A PHE* 1.3 75.7 - - - +
216A SER* 1.3 57.1 + - - +
218A SER* 2.7 31.2 + - - +
219A ARG* 3.2 27.5 + - - +
249A ARG* 3.3 24.7 + - - +
251A LYS 4.6 0.5 - - - +
252A TYR* 3.4 22.3 - - + -
253A SER* 2.7 48.8 + - - -
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Residues in contact with SER 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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99A GLU* 3.1 38.0 + - - -
141A PHE* 3.0 25.3 - - - -
178A PRO* 3.7 17.1 - - - +
214A PHE* 3.3 10.7 - - - -
215A GLU* 1.3 78.1 - - - +
217A ILE* 1.3 61.4 + - - +
218A SER 3.3 0.7 + - - -
219A ARG* 3.9 13.6 + - - +
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Residues in contact with ILE 217 (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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141A PHE* 3.5 17.7 - - + -
178A PRO* 3.8 18.6 - - + -
179A LEU 4.2 0.2 - - - -
180A LYS* 3.9 51.8 + - + +
212A ALA 3.8 23.6 - - - +
213A ARG* 4.3 1.8 - - - -
214A PHE* 3.3 51.4 - - + +
216A SER* 1.3 78.2 + - - +
218A SER* 1.3 60.5 + - - +
219A ARG 3.5 1.1 - - - -
220A ILE* 3.4 15.8 - - - +
247A GLY* 4.8 1.7 - - - +
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Residues in contact with SER 218 (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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213A ARG* 5.9 1.6 - - - -
214A PHE 4.1 7.2 - - - -
215A GLU 2.7 19.2 + - - -
217A ILE* 1.3 81.4 - - - +
219A ARG* 1.3 56.6 + - - +
220A ILE* 3.0 15.6 + - - +
247A GLY 3.1 23.5 - - - +
248A LEU* 3.7 1.2 - - - +
249A ARG* 3.4 25.2 - - - +
252A TYR* 2.6 40.3 + - - -
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Residues in contact with ARG 219 (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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140A PRO* 4.0 2.6 - - - +
141A PHE* 3.5 23.1 - - + -
215A GLU* 3.2 41.1 + - - +
216A SER* 3.9 9.6 + - - +
217A ILE 3.5 1.6 - - - -
218A SER* 1.3 75.1 - - - +
220A ILE* 1.3 59.3 + - - +
221A GLU* 3.2 19.6 + - - +
252A TYR* 3.8 24.2 - - + +
253A SER* 4.2 3.8 - - - +
254A ASP* 2.9 43.9 + - - +
256A LYS* 4.0 2.0 - - - +
261A TYR* 3.0 43.2 + - + +
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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