Contacts of the helix formed by residues 222 - 235 (chain A) in PDB entry 4QGC
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 SER 222 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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115A LYS* 6.1 0.5 - - - +
116A GLY 4.9 5.7 + - - -
117A PRO* 6.3 0.2 - - - -
219A PRO* 4.2 21.8 + - - -
220A ALA 4.0 1.2 - - - -
221A VAL* 1.3 76.7 - - - +
223A GLU* 1.3 60.1 + - - +
224A LYS* 3.5 9.8 + - - +
225A ASP* 3.0 33.7 + - - -
226A ILE* 3.0 27.8 + - - +
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Residues in contact with GLU 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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222A SER* 1.3 73.0 - - - +
224A LYS* 1.3 63.9 + - - +
226A ILE* 3.4 14.1 + - + +
227A GLN* 3.2 43.3 + - + +
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Residues in contact with LYS 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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76A PHE* 3.2 19.3 + - - +
77A SER 5.5 2.5 - - - -
79A GLY 5.3 5.9 + - - -
115A LYS* 3.7 32.8 - - + +
222A SER* 3.5 9.3 + - - +
223A GLU* 1.3 80.0 - - - +
225A ASP* 1.3 57.4 + - - +
227A GLN* 3.3 18.4 + - - +
228A ASP* 2.8 66.0 + - - +
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Residues in contact with ASP 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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114A THR* 4.5 11.5 - - + -
115A LYS* 3.9 14.2 + - - +
116A GLY* 3.3 38.6 + - - +
220A ALA 3.6 7.2 - - - +
221A VAL* 3.9 11.7 - - + -
222A SER* 3.0 36.4 + - - +
224A LYS* 1.3 78.0 - - - +
226A ILE* 1.3 60.1 + - - +
228A ASP* 3.1 8.6 + - - +
229A LEU* 2.8 36.2 + - + +
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Residues in contact with ILE 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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221A VAL* 3.9 17.3 - - + +
222A SER 3.0 17.3 + - - +
223A GLU* 3.6 16.8 - - + +
224A LYS 3.3 0.2 - - - -
225A ASP* 1.3 76.8 - - - +
227A GLN* 1.3 64.4 + - + +
229A LEU* 3.3 1.4 + - - +
230A LYS* 3.0 34.3 + - + +
257A VAL* 3.9 29.3 - - + +
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Residues in contact with GLN 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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81A HIS* 3.4 19.4 - - + -
223A GLU* 3.2 31.7 + - + +
224A LYS* 3.4 22.0 - - - +
225A ASP 3.3 0.2 - - - -
226A ILE* 1.3 79.7 - - + +
228A ASP* 1.3 62.1 + - - +
230A LYS* 3.8 5.9 - - - +
231A PHE* 3.1 21.1 + - - +
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Residues in contact with ASP 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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76A PHE* 3.3 33.8 - - + +
81A HIS* 3.1 21.6 + - - -
112A LEU* 3.4 18.2 - - + +
114A THR* 5.5 2.5 - - + -
115A LYS 4.9 1.6 + - - -
224A LYS* 2.8 47.2 + - - +
225A ASP* 3.1 14.7 + - - +
227A GLN* 1.3 77.3 - - - +
229A LEU* 1.3 60.0 + - + +
231A PHE* 3.2 4.8 + - - +
232A GLY 3.0 21.8 + - - -
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Residues in contact with LEU 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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112A LEU* 4.3 4.3 - - + -
114A THR* 3.8 16.6 - - + -
221A VAL* 4.4 14.8 - - + -
225A ASP* 2.8 24.4 + - + +
228A ASP* 1.3 68.7 - - - +
230A LYS* 1.3 65.2 + - - +
232A GLY* 3.1 3.7 + - - +
233A VAL* 3.1 27.6 + - - +
240A VAL* 3.8 39.5 - - + -
254A VAL* 4.1 23.3 - - + +
257A VAL* 3.8 36.3 - - + -
258A LEU* 4.0 11.9 - - + +
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Residues in contact with LYS 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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226A ILE* 3.0 32.7 + - + +
227A GLN* 3.8 6.1 - - - +
229A LEU* 1.3 73.2 - - - +
231A PHE* 1.3 65.8 + - - +
233A VAL* 3.2 20.0 + - + +
234A GLU* 3.1 39.6 + - - +
257A VAL* 4.2 22.8 + - + +
258A LEU 5.5 1.6 + - - -
261A LYS* 4.5 24.2 - - - +
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Residues in contact with PHE 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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76A PHE* 3.5 34.5 - + - -
81A HIS* 3.3 57.4 - + + +
84A HIS* 4.0 7.9 - - + -
85A ALA* 3.8 10.1 - - + -
88A ILE* 4.3 7.9 - - + -
112A LEU* 4.7 0.4 - - + -
227A GLN 3.1 15.2 + - - +
228A ASP 3.4 7.2 - - - +
230A LYS* 1.3 75.4 - - - +
232A GLY* 1.3 59.4 + - - +
234A GLU* 3.4 15.7 + - + +
235A GLN* 2.9 65.7 + - + +
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Residues in contact with GLY 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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112A LEU* 3.7 22.2 - - - -
228A ASP 3.0 10.5 + - - -
229A LEU* 3.1 5.9 + - - -
231A PHE* 1.3 78.5 - - - +
233A VAL* 1.3 59.0 + - - +
235A GLN* 3.5 0.4 + - - -
236A ASP 3.1 3.6 + - - -
237A VAL* 3.1 47.2 + - - +
240A VAL* 6.2 0.7 - - - -
258A LEU* 5.9 0.4 - - - -
265A ILE* 4.4 1.1 - - - +
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Residues in contact with VAL 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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229A LEU 3.1 16.7 + - - +
230A LYS* 3.2 22.6 + - + +
232A GLY* 1.3 77.2 - - - +
234A GLU* 1.3 65.4 + - + +
236A ASP* 3.1 15.1 + - - +
258A LEU* 3.8 33.9 - - + +
261A LYS* 3.9 38.6 - - + +
262A GLY* 4.4 2.2 - - - +
265A ILE* 4.3 11.9 - - + -
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Residues in contact with GLU 234 (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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230A LYS* 3.1 28.4 + - - +
231A PHE* 3.4 16.3 + - - +
233A VAL* 1.3 78.6 - - + +
235A GLN* 1.3 64.0 + - + +
236A ASP* 3.2 2.9 + - - +
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Residues in contact with GLN 235 (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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85A ALA* 4.0 16.3 - - - +
88A ILE* 3.9 33.3 - - + +
92A ARG* 2.6 43.0 + - - +
231A PHE* 2.9 59.7 + - + +
232A GLY 4.1 3.4 - - - +
233A VAL 3.2 0.2 - - - -
234A GLU* 1.3 79.2 + - + +
236A ASP* 1.3 54.9 + - - +
237A VAL* 3.4 4.6 + - + +
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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