Contacts of the helix formed by residues 222 - 235 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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115D LYS* 5.8 1.4 - - - +
116D GLY 4.7 10.9 + - - -
117D PRO* 5.2 5.1 - - - -
219D PRO* 4.5 14.1 + - - -
220D ALA 4.0 1.2 - - - -
221D VAL* 1.3 78.2 - - - +
223D GLU* 1.3 63.2 + - - +
224D LYS* 3.4 10.0 + - - +
225D ASP* 2.9 45.4 + - - -
226D ILE* 3.0 11.3 + - - +
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Residues in contact with GLU 223 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221D VAL 3.9 0.5 + - - +
222D SER* 1.3 73.2 - - - +
224D LYS* 1.3 61.5 + - - +
226D ILE* 3.6 24.2 + - + +
227D GLN* 3.3 24.9 + - + +
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Residues in contact with LYS 224 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76D PHE* 2.5 32.5 + - - +
77D SER 4.5 4.2 + - - -
78D HIS* 5.0 0.4 - - - +
79D GLY 5.0 8.6 + - - -
81D HIS* 5.8 0.9 - - - -
115D LYS* 4.0 29.4 - - + +
222D SER* 3.0 8.8 + - - +
223D GLU* 1.3 78.6 - - - +
225D ASP* 1.3 59.4 + - - +
227D GLN* 3.2 11.4 + - + +
228D ASP* 3.0 59.0 + - - +
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Residues in contact with ASP 225 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114D THR* 4.1 10.7 - - - -
115D LYS* 3.7 14.9 + - - +
116D GLY* 3.2 36.1 + - - -
220D ALA 3.9 7.6 - - - +
221D VAL* 3.6 16.4 - - + -
222D SER* 2.9 36.6 + - - +
224D LYS* 1.3 75.8 - - - +
226D ILE* 1.3 56.2 + - - +
228D ASP* 3.1 8.2 + - - +
229D LEU* 2.8 42.8 + - + +
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Residues in contact with ILE 226 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221D VAL* 3.6 23.3 - - + +
222D SER 3.0 14.5 + - - +
223D GLU* 3.7 29.8 - - + +
225D ASP* 1.3 76.0 - - - +
227D GLN* 1.3 64.0 + - + +
229D LEU* 4.2 0.9 - - - +
230D LYS* 3.2 37.3 + - - +
257D VAL* 4.3 25.9 - - + +
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Residues in contact with GLN 227 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81D HIS* 3.5 16.2 - - + +
223D GLU* 3.3 16.8 - - + +
224D LYS* 3.2 13.2 + - + +
225D ASP 3.1 0.4 - - - -
226D ILE* 1.3 79.8 - - + +
228D ASP* 1.3 59.6 + - - +
230D LYS* 3.4 22.8 + - - +
231D PHE* 3.0 27.0 + - - +
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Residues in contact with ASP 228 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76D PHE* 3.4 29.8 - - + +
81D HIS* 2.6 34.3 + - - -
112D LEU* 3.5 17.9 - - + +
114D THR* 5.7 2.2 - - + -
115D LYS 4.8 1.9 + - - -
224D LYS* 3.0 51.5 + - - +
225D ASP* 3.1 13.3 + - - +
227D GLN* 1.3 77.9 - - - +
229D LEU* 1.3 57.6 + - + +
231D PHE* 3.3 3.8 + - - +
232D GLY 2.9 22.7 + - - -
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Residues in contact with LEU 229 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112D LEU* 4.4 4.0 - - + -
114D THR* 4.0 15.5 - - + -
221D VAL* 4.0 17.7 - - + -
225D ASP* 2.8 25.8 + - + +
228D ASP* 1.3 69.8 - - - +
230D LYS* 1.3 65.9 + - - +
232D GLY* 3.2 3.6 + - - +
233D VAL* 3.2 27.8 + - - +
240D VAL* 3.7 41.3 - - + -
254D VAL* 4.0 23.1 - - + +
257D VAL* 3.9 30.3 - - + -
258D LEU* 4.0 14.0 - - + +
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Residues in contact with LYS 230 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226D ILE* 3.2 29.8 + - - +
227D GLN* 3.5 25.1 - - - +
228D ASP 3.3 0.2 - - - -
229D LEU* 1.3 78.7 - - - +
231D PHE* 1.3 61.5 + - - +
233D VAL* 3.1 14.6 + - - +
234D GLU* 3.1 36.8 + - - +
257D VAL* 5.0 5.4 - - + +
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Residues in contact with PHE 231 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76D PHE* 3.7 35.0 - + - -
81D HIS* 3.3 53.8 - + + -
84D HIS* 4.4 5.8 - - + -
85D ALA* 3.6 15.0 - - + -
88D ILE* 4.5 4.5 - - + -
112D LEU* 5.1 0.2 - - + -
227D GLN 3.0 13.8 + - - +
228D ASP 3.4 7.2 - - - +
230D LYS* 1.3 78.1 - - - +
232D GLY* 1.3 61.9 + - - +
234D GLU* 3.3 10.8 + - + +
235D GLN* 3.1 62.6 + - + +
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Residues in contact with GLY 232 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112D LEU* 3.6 24.0 - - - +
228D ASP 2.9 10.5 + - - -
229D LEU* 3.2 5.5 + - - -
231D PHE* 1.3 77.9 - - - +
233D VAL* 1.3 60.1 + - - +
235D GLN* 3.4 1.5 + - - -
236D ASP 3.2 4.0 + - - -
237D VAL* 3.2 43.5 + - - +
240D VAL* 6.2 0.7 - - - -
258D LEU* 6.0 0.4 - - - -
265D ILE* 4.8 0.4 - - - -
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Residues in contact with VAL 233 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229D LEU 3.3 15.5 - - - +
230D LYS* 3.1 11.4 + - + +
232D GLY* 1.3 76.8 - - - +
234D GLU* 1.3 67.9 + - - +
236D ASP* 3.3 13.0 + - - +
257D VAL 5.5 0.4 - - - +
258D LEU* 3.9 34.5 - - + +
261D LYS* 3.8 40.8 - - + +
262D GLY* 4.4 1.3 - - - -
265D ILE* 4.2 13.2 - - + -
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Residues in contact with GLU 234 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230D LYS* 3.1 38.7 - - + +
231D PHE* 3.3 12.8 + - + +
233D VAL* 1.3 83.9 - - - +
235D GLN* 1.3 67.4 + - + +
236D ASP* 3.2 3.2 + - - +
261D LYS* 5.8 3.1 - - - +
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Residues in contact with GLN 235 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85D ALA* 4.2 13.5 - - - +
88D ILE* 3.6 35.4 - - + +
92D ARG* 2.5 43.0 + - - +
231D PHE* 3.1 59.4 + - + +
232D GLY 3.4 4.2 + - - +
233D VAL 3.2 0.4 - - - -
234D GLU* 1.3 80.3 + - - +
236D ASP* 1.3 55.2 + - - +
237D VAL* 3.4 5.2 + - + +
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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