Contacts of the helix formed by residues 220 - 233 (chain A) in PDB entry 4H3E
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 ASP 220 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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115A ARG 3.9 16.9 - - - +
116A CYS 2.8 12.2 + - - +
117A ILE 5.3 0.2 - - - +
118A THR* 3.8 19.1 - - + -
122A LYS* 3.5 28.6 - - - +
218A VAL 3.4 1.4 + - - -
219A ILE* 1.3 70.0 - - - +
221A TRP* 1.3 60.7 + - - +
222A GLU* 3.0 21.5 + - - +
223A PHE* 3.1 19.2 + - - +
224A VAL* 3.2 21.3 + - - +
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Residues in contact with TRP 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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122A LYS 3.1 28.8 + - - +
123A ALA* 4.5 0.9 - - - -
124A MET* 3.5 51.3 - - + +
125A PRO* 3.6 3.6 - - - +
128A PHE* 3.8 32.2 - + + -
142A PHE* 4.1 13.0 - + - -
143A LYS* 4.2 12.2 - - - +
191A LEU* 4.1 11.7 - - + -
216A TRP* 3.7 47.2 + + - -
219A ILE* 3.6 28.5 - - + +
220A ASP* 1.3 69.8 - - - +
222A GLU* 1.3 58.8 + - - +
224A VAL* 3.7 16.4 - - + +
225A ALA* 2.8 30.3 + - - +
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Residues in contact with GLU 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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122A LYS* 3.3 29.4 - - + +
123A ALA 4.0 16.1 + - - +
125A PRO* 4.4 11.2 - - + -
220A ASP* 3.0 7.9 + - - +
221A TRP* 1.3 76.8 - - - +
223A PHE* 1.3 65.2 + - - +
225A ALA* 3.4 5.6 + - - +
226A LYS* 3.0 24.1 + - - +
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Residues in contact with PHE 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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23A LEU* 4.5 7.0 - - + -
112A PHE* 3.8 25.4 - + - -
115A ARG* 3.4 60.1 - - + +
116A CYS* 3.9 15.5 - - - -
220A ASP* 3.1 19.5 + - - +
222A GLU* 1.3 74.3 - - - +
224A VAL* 1.3 69.1 + - - +
226A LYS* 3.3 11.8 + - + +
227A MET* 3.0 66.4 + - + +
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Residues in contact with VAL 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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116A CYS* 4.5 7.6 - - - -
128A PHE* 3.5 31.9 - - + -
161A LEU* 5.3 0.2 - - + -
190A VAL* 3.2 35.2 - - + +
191A LEU* 4.1 15.5 - - + -
219A ILE* 4.1 10.5 - - + -
220A ASP 3.2 14.2 + - - +
221A TRP* 3.7 25.4 - - + +
222A GLU 3.3 0.2 - - - -
223A PHE* 1.3 76.1 - - + +
225A ALA* 1.3 56.2 + - - +
227A MET* 3.2 5.0 + - - +
228A HIS* 2.9 26.2 + - - +
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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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125A PRO* 3.6 26.2 - - + -
128A PHE* 3.7 27.3 - - + +
221A TRP 2.8 22.5 + - - +
222A GLU 3.7 3.4 - - - +
224A VAL* 1.3 73.3 - - - +
226A LYS* 1.3 57.0 + - - +
228A HIS* 3.1 4.0 + - - +
229A ALA* 2.8 30.5 + - - +
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Residues in contact with LYS 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 GLU 3.0 17.8 + - - +
223A PHE* 3.6 12.2 - - + +
225A ALA* 1.3 72.0 - - - +
227A MET* 1.3 80.4 + - + +
229A ALA* 3.3 6.7 + - + +
230A GLN* 3.0 52.0 + - + +
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Residues in contact with MET 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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20A TYR* 3.9 5.8 + - - -
22A THR* 3.6 37.2 - - - +
23A LEU* 4.6 3.8 - - + -
112A PHE* 3.7 8.3 - - + -
189A PRO 4.0 3.9 - - - +
190A VAL* 3.8 19.2 - - - +
223A PHE* 3.0 57.0 + - + +
224A VAL 3.5 7.4 - - - +
226A LYS* 1.3 93.8 - - + +
228A HIS* 1.3 58.0 + - - +
230A GLN* 3.7 20.6 - - - +
231A ALA* 2.9 31.2 + - - +
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Residues in contact with HIS 228 (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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127A SER* 5.5 1.3 - - - -
128A PHE* 3.7 30.0 - + + -
131A ALA* 3.6 25.8 - - + +
163A VAL* 3.8 6.1 - - + +
169A ASN 5.3 2.5 - - - -
171A LEU* 3.8 32.4 - - + +
190A VAL* 3.6 10.9 - - + +
224A VAL 2.9 12.7 + - - +
225A ALA 3.1 8.7 + - - +
227A MET* 1.3 77.8 - - - +
229A ALA* 1.3 66.4 + - + +
231A ALA* 3.2 2.6 + - - +
232A ILE* 3.2 55.9 + - + +
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Residues in contact with ALA 229 (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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225A ALA 2.8 19.6 + - - +
226A LYS* 3.8 8.3 - - + +
228A HIS* 1.3 75.0 - - + +
230A GLN* 1.3 64.6 + - + +
232A ILE* 3.4 12.4 - - - +
233A LYS* 3.3 21.5 + - - +
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Residues in contact with GLN 230 (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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20A TYR* 3.6 26.6 + - + +
22A THR 4.8 4.9 - - - +
24A PRO* 6.0 1.0 - - - +
188A ARG* 4.7 0.9 + - - -
226A LYS* 3.0 47.7 + - + +
227A MET* 3.7 19.8 - - - +
229A ALA* 1.3 78.4 - - + +
231A ALA* 1.3 61.9 + - - +
232A ILE 3.4 0.3 + - - -
233A LYS* 3.4 17.7 + - - +
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Residues in contact with ALA 231 (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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20A TYR* 3.4 17.4 + - - +
163A VAL* 3.8 25.7 - - + +
169A ASN* 4.7 2.4 - - - +
188A ARG* 2.8 46.0 + - + -
189A PRO 5.5 1.1 - - - +
190A VAL* 4.7 2.7 - - + -
227A MET 2.9 19.9 + - - +
228A HIS 3.2 5.1 + - - +
230A GLN* 1.3 78.3 - - - +
232A ILE* 1.3 57.8 - - - +
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Residues in contact with ILE 232 (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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163A VAL* 4.1 8.5 - - + -
169A ASN* 3.7 41.3 + - + +
228A HIS* 3.2 45.0 + - + +
229A ALA* 3.4 16.8 - - - +
231A ALA* 1.3 78.6 - - - +
233A LYS* 1.3 67.4 + - - +
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Residues in contact with LYS 233 (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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188A ARG* 5.1 5.0 + - - -
229A ALA 3.3 13.8 + - - +
230A GLN* 3.4 17.0 + - - +
231A ALA 3.6 1.6 - - - +
232A ILE* 1.3 83.6 - - - +
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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