Contacts of the helix formed by residues 278 - 291 (chain D) in PDB entry 1QGN
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 LEU 278 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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130D GLU* 2.7 46.8 + - + +
131D SER* 4.2 10.1 - - - +
276D GLY 3.8 0.2 + - - -
277D PRO* 1.3 69.9 - - - +
279D LYS* 1.3 64.1 + - - +
281D VAL* 3.6 8.7 - - + -
282D SER* 2.8 39.7 + - - -
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Residues in contact with LYS 279 (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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130D GLU* 4.1 2.5 + - - +
277D PRO* 3.3 6.2 - - + -
278D LEU* 1.3 80.2 - - - +
280D LEU* 1.3 69.0 + - + +
282D SER* 4.1 6.2 + - - -
283D GLU* 3.6 19.4 - - - +
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Residues in contact with LEU 280 (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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149D LEU* 4.3 15.3 - - + +
232D LEU* 3.8 35.2 - - + -
253D ASP* 4.2 7.6 - - + +
254D LEU* 3.7 34.1 - - + -
277D PRO* 3.0 23.9 + - + +
279D LYS* 1.3 90.8 - - + +
281D VAL* 1.3 62.2 + - - +
282D SER 3.1 1.8 - - - -
283D GLU* 3.0 28.7 + - + +
284D ILE* 3.5 10.7 + - - +
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Residues in contact with VAL 281 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131D SER* 2.9 45.3 - - - +
133D LEU* 3.9 18.7 - - + +
254D LEU* 4.5 4.2 - - + +
274D ILE* 3.7 30.1 - - + +
276D GLY 4.7 4.7 - - - +
277D PRO 2.8 22.1 + - - +
278D LEU* 3.6 5.2 - - + +
280D LEU* 1.3 74.9 - - - +
282D SER* 1.3 61.1 + - - +
284D ILE* 3.4 11.8 + - + +
285D ARG* 3.0 26.9 + - - +
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Residues in contact with SER 282 (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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278D LEU* 2.8 31.0 + - - -
279D LYS* 4.1 6.1 + - - -
281D VAL* 1.3 78.4 - - - +
283D GLU* 1.3 68.8 + - - +
285D ARG* 3.5 13.3 - - - +
286D ASN* 3.1 31.6 + - - +
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Residues in contact with GLU 283 (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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148D ALA* 4.1 16.5 - - - +
149D LEU* 4.5 15.0 - - + -
279D LYS 3.6 15.7 - - - +
280D LEU* 3.0 14.6 + - + +
282D SER* 1.3 83.3 + - - +
284D ILE* 1.3 61.6 - - - +
286D ASN* 3.7 26.5 + - - +
287D LEU* 3.7 4.2 + - - +
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Residues in contact with ILE 284 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133D LEU* 3.7 16.6 - - + -
135D MET* 4.0 4.3 - - + -
144D VAL* 3.6 22.8 - - + +
145D MET* 4.0 30.3 - - + -
148D ALA* 4.0 10.3 - - + -
149D LEU* 4.2 22.7 - - + -
254D LEU* 4.5 5.4 - - + -
274D ILE* 4.1 23.8 - - + -
280D LEU 3.8 13.5 - - - +
281D VAL* 3.4 11.6 + - - +
282D SER 3.2 0.2 - - - -
283D GLU* 1.3 76.9 - - - +
285D ARG* 1.3 66.9 + - - +
286D ASN 3.0 2.5 + - - -
287D LEU* 3.1 3.8 + - - +
288D HIS* 2.9 19.9 + - - +
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Residues in contact with ARG 285 (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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111D TYR 5.5 2.8 + - - -
120D GLU* 2.9 32.7 + - - -
131D SER* 3.4 17.8 + - - -
132D THR 3.2 20.6 + - - -
133D LEU* 3.3 27.7 - - + +
281D VAL* 3.0 19.5 + - - +
282D SER* 3.5 13.3 - - - +
284D ILE* 1.3 78.1 - - - +
286D ASN* 1.3 65.8 + - - +
288D HIS* 3.0 21.7 - - - +
289D HIS* 3.1 39.4 + - + -
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Residues in contact with ASN 286 (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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282D SER* 3.1 21.3 + - - +
283D GLU* 3.7 24.8 + - - +
284D ILE 3.0 0.4 - - - -
285D ARG* 1.3 78.2 - - - +
287D LEU* 1.3 64.8 + - - +
288D HIS 2.9 4.3 - - - -
289D HIS* 2.8 28.9 + - - +
290D ILE* 3.5 9.8 + - - +
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Residues in contact with LEU 287 (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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173B ILE* 4.1 30.1 - - + -
144D VAL* 3.5 26.0 - - + +
147D LEU* 3.7 12.8 - - + +
148D ALA* 3.6 26.5 - - + +
283D GLU 3.7 3.6 + - - +
284D ILE 3.1 7.0 + - - +
286D ASN* 1.3 78.8 - - - +
288D HIS* 1.3 56.4 + - - +
290D ILE* 3.1 15.6 + - + +
291D LEU* 2.9 60.1 + - + +
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Residues in contact with HIS 288 (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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110D ARG 4.9 5.0 + - - +
133D LEU* 3.8 27.6 - - + -
134D LEU 3.9 11.2 + - - -
135D MET* 3.5 32.4 - - + +
144D VAL* 4.3 9.3 - - - +
284D ILE 2.9 13.1 + - - +
285D ARG* 3.0 14.6 - - - +
286D ASN 2.9 0.4 - - - -
287D LEU* 1.3 79.7 - - - +
289D HIS* 1.3 66.2 + + - +
291D LEU* 4.5 2.4 - - - +
292D GLY* 2.8 32.2 + - - +
293D GLY* 3.6 34.5 + - - -
294D ALA* 3.8 11.1 - - - +
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Residues in contact with HIS 289 (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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165B LYS* 4.3 9.6 - - - +
110D ARG* 3.1 51.7 + - - -
111D TYR* 3.5 46.1 + + + -
285D ARG* 3.1 40.8 + - + +
286D ASN* 2.8 18.4 + - - +
288D HIS* 1.3 85.8 - + - +
290D ILE* 1.3 58.3 + - + +
292D GLY 4.2 0.9 - - - -
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Residues in contact with ILE 290 (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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139B MET* 3.2 28.3 - - + +
143B THR* 4.2 1.0 + - - -
165B LYS* 4.2 30.7 - - + +
168B ILE* 3.8 26.9 - - + -
169B PHE* 3.9 39.3 - - + +
172B THR* 5.4 3.1 - - - +
173B ILE* 5.5 3.4 - - + -
286D ASN 3.5 10.3 + - - +
287D LEU* 3.1 18.7 + - + +
288D HIS 3.1 0.4 - - - -
289D HIS* 1.3 80.7 - - - +
291D LEU* 1.3 66.0 + - + +
292D GLY 3.1 1.7 + - - -
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Residues in contact with LEU 291 (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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140B CYS* 3.4 26.4 - - - +
143B THR* 3.3 32.5 - - + +
147B LEU* 5.1 4.5 - - + -
169B PHE* 3.7 23.1 - - + -
173B ILE* 5.9 0.4 - - + -
143D THR* 5.9 0.7 - - + -
144D VAL* 4.0 24.2 - - + -
147D LEU* 4.4 14.6 - - + -
287D LEU* 2.9 51.1 + - + +
288D HIS* 4.5 1.6 - - - +
290D ILE* 1.3 75.7 - - - +
292D GLY* 1.3 63.9 + - - +
293D GLY* 3.4 3.5 + - - +
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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