Contacts of the helix formed by residues 214 - 227 (chain A) in PDB entry 5W5T
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 THR 214 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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122A ILE* 4.4 5.6 - - + -
123A GLU* 5.9 2.2 - - + -
126A ALA* 5.9 0.4 - - - -
127A PRO* 2.6 41.2 + - + +
128A GLU 2.8 20.3 + - - -
129A TYR 3.2 11.8 + - - -
130A MET* 3.6 21.8 - - + +
213A HIS* 1.3 72.8 - - - +
215A LYS* 1.3 66.4 + - + +
217A LEU* 3.5 2.9 + - - +
218A MET* 3.1 43.2 + - + +
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Residues in contact with LYS 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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128A GLU* 5.5 7.2 - - - -
213A HIS* 3.5 1.4 - - + +
214A THR* 1.3 79.0 - - + +
216A PHE* 1.3 76.4 + - + +
218A MET* 3.4 9.5 + - + +
219A GLU* 3.3 21.5 + - - +
222A ARG* 5.2 0.9 + - - -
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Residues in contact with PHE 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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154A GLY 6.0 0.9 - - - -
155A ALA 4.9 3.8 - - - -
156A ASP* 4.2 35.4 - - + +
212A PHE* 5.6 2.5 - - + -
213A HIS* 3.3 50.0 + + + +
214A THR 3.4 0.2 - - - -
215A LYS* 1.3 87.9 - - + +
217A LEU* 1.3 51.1 + - - +
219A GLU* 3.3 9.0 + - - +
220A ALA* 2.8 34.0 + - - +
223A ARG* 5.0 1.4 + - - -
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Residues in contact with LEU 217 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115A VAL* 4.7 5.6 - - + -
130A MET* 3.7 29.2 - - + -
132A ILE* 4.0 13.5 - - + -
212A PHE* 3.4 54.0 - - + +
213A HIS 3.6 10.3 + - - +
214A THR 3.5 7.8 + - - +
215A LYS 3.3 0.2 - - - -
216A PHE* 1.3 74.8 - - - +
218A MET* 1.3 65.1 + - + +
220A ALA* 2.8 8.5 + - + +
221A LEU* 2.7 64.1 + - + +
234A PHE* 3.8 6.1 - - + -
238A ILE* 5.1 0.7 - - + -
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Residues in contact with MET 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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115A VAL* 4.2 13.7 - - + -
119A ILE* 3.8 37.2 - - - +
122A ILE* 4.0 25.4 - - + -
123A GLU* 4.0 16.4 - - + +
130A MET* 4.6 1.1 - - + -
214A THR* 3.1 35.8 + - + +
215A LYS* 3.6 10.8 - - + +
217A LEU* 1.3 88.6 - - + +
219A GLU* 1.3 57.4 + - - +
221A LEU* 3.3 4.7 + - + +
222A ARG* 3.0 53.2 + - - +
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Residues in contact with GLU 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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215A LYS 3.3 10.0 + - - +
216A PHE* 3.6 9.5 - - - +
217A LEU 3.2 0.4 - - - -
218A MET* 1.3 75.6 - - - +
220A ALA* 1.3 56.8 + - - +
222A ARG* 3.0 15.3 + - + +
223A ARG* 2.8 54.6 + - + +
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Residues in contact with ALA 220 (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 PHE* 5.7 2.0 - - + -
216A PHE 2.8 16.5 + - - +
217A LEU* 2.8 16.1 + - + +
219A GLU* 1.3 76.0 - - - +
221A LEU* 1.3 62.0 + - + +
223A ARG* 3.8 25.9 + - - +
224A ASP* 3.4 21.8 + - - +
238A ILE* 3.6 20.3 - - + +
242A ILE* 4.9 9.9 - - + -
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Residues in contact with LEU 221 (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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112A ALA* 2.8 40.2 - - + +
115A VAL* 3.4 24.7 - - + -
116A TYR* 3.6 20.7 - - + +
119A ILE* 5.2 2.2 - - + -
217A LEU* 2.7 62.4 + - + +
218A MET* 3.9 4.7 - - - +
220A ALA* 1.3 73.6 - - + +
222A ARG* 1.3 60.6 + - - +
223A ARG 3.3 0.2 - - - -
224A ASP* 3.4 5.5 + - - +
225A ALA* 3.0 26.7 + - - +
232A ARG* 4.6 0.9 + - - -
234A PHE* 4.2 4.5 - - + -
238A ILE* 4.0 15.3 - - + -
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Residues in contact with ARG 222 (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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116A TYR* 4.2 20.2 - - + -
119A ILE* 4.1 15.2 - - + +
123A GLU* 3.0 31.4 + - - -
215A LYS 5.2 0.8 + - - -
218A MET* 3.0 40.2 + - - +
219A GLU* 3.4 15.8 - - + +
221A LEU* 1.3 74.4 - - - +
223A ARG* 1.3 64.9 + - - +
225A ALA* 3.0 13.5 + - - +
226A ALA* 3.2 13.5 + - - +
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Residues in contact with ARG 223 (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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216A PHE 5.0 1.4 + - - -
219A GLU* 2.8 33.9 + - + +
220A ALA* 3.8 33.1 + - - +
222A ARG* 1.3 77.5 - - - +
224A ASP* 1.3 59.6 + - - +
226A ALA* 3.3 8.7 + - + +
227A ASP* 3.2 23.3 + - + +
241A TYR* 3.3 51.0 + - + -
242A ILE* 4.7 6.3 - - - +
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Residues in contact with ASP 224 (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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112A ALA* 3.8 6.5 - - + +
220A ALA 3.4 14.8 + - - +
221A LEU* 3.6 6.3 - - - +
222A ARG 3.1 0.8 - - - -
223A ARG* 1.3 76.6 - - - +
225A ALA* 1.3 65.1 + - - +
226A ALA 3.4 0.2 + - - -
227A ASP* 3.5 20.8 + - - +
230A SER* 2.3 28.8 + - - -
232A ARG* 2.7 44.8 + - - +
237A ASP* 3.5 11.3 - - - +
238A ILE* 3.8 18.9 + - + +
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Residues in contact with ALA 225 (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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116A TYR* 3.5 43.5 - - + +
221A LEU 3.0 7.5 + - - +
222A ARG 3.0 10.1 + - - +
224A ASP* 1.3 78.4 + - - +
226A ALA* 1.3 61.0 + - - +
227A ASP 4.6 1.9 - - - +
232A ARG* 3.8 21.0 + - - +
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Residues in contact with ALA 226 (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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222A ARG 3.2 10.4 + - - +
223A ARG* 3.6 10.8 - - - +
224A ASP 3.2 0.4 - - - -
225A ALA* 1.3 78.0 - - - +
227A ASP* 1.3 58.2 + - - +
228A PRO* 3.2 12.8 - - - +
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Residues in contact with ASP 227 (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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223A ARG* 3.2 14.5 + - + +
224A ASP* 3.5 9.1 + - - +
225A ALA 3.4 2.7 - - - +
226A ALA* 1.3 76.1 - - - +
228A PRO* 1.3 70.9 - - - +
229A THR* 3.1 21.0 + - - +
230A SER* 2.7 50.2 + - - +
232A ARG* 5.1 1.6 - - - -
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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