Contacts of the helix formed by residues 424 - 442 (chain D) in PDB entry 3G1Q
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 GLY 424 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134D LEU* 4.2 4.9 - - - -
422D CYS* 3.3 8.1 - - - -
423D ILE* 1.4 80.4 - - - +
425D GLN* 1.3 59.4 + - - +
426D LYS 3.3 2.5 - - - -
427D PHE* 3.2 8.3 + - - +
428D GLY* 2.8 29.8 + - - -
480D HEM 3.6 34.8 - - - +
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Residues in contact with GLN 425 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347D ARG* 3.2 23.0 + - - -
415D PHE* 3.5 57.5 + - + +
416D GLY 5.8 0.4 + - - -
421D LYS* 5.7 5.5 - - - +
422D CYS* 3.3 25.6 + - - +
423D ILE 3.4 1.6 - - - -
424D GLY* 1.3 77.9 - - - +
426D LYS* 1.3 72.2 + - + +
428D GLY* 3.8 0.3 - - - -
429D LEU* 3.0 38.3 + - + +
480D HEM 4.9 0.9 - - - -
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Residues in contact with LYS 426 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409B GLU* 2.5 42.1 + - - +
134D LEU 5.5 1.6 - - - +
135D THR* 6.2 0.7 - - - -
136D ILE* 5.2 12.6 - - + +
139D PHE* 3.5 20.8 - - + -
336D MET* 5.0 7.1 - - - +
423D ILE 5.3 0.6 + - - -
424D GLY 3.3 0.6 - - - -
425D GLN* 1.3 91.1 + - + +
427D PHE* 1.3 58.4 + - - +
429D LEU* 3.6 7.3 + - + +
430D LEU* 2.9 27.9 + - - +
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Residues in contact with PHE 427 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134D LEU* 4.3 15.4 + - + +
139D PHE* 3.3 17.5 - + + -
142D PHE* 3.7 29.6 - + + -
146D ILE* 4.9 0.9 - - + -
179D ALA* 4.1 11.0 - - + -
182D CYS* 3.7 34.8 - - + -
183D LEU* 4.1 25.4 - - + -
424D GLY* 3.2 10.0 + - - +
426D LYS* 1.3 76.2 - - - +
428D GLY* 1.3 67.1 + - - +
430D LEU* 3.2 7.7 + - + +
431D GLN* 3.1 52.1 + - + +
480D HEM 3.9 26.9 - - + -
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Residues in contact with GLY 428 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296D SER* 3.7 20.9 + - - -
424D GLY 2.8 16.9 + - - -
425D GLN 3.8 1.8 - - - -
427D PHE* 1.3 75.7 - - - +
429D LEU* 1.3 56.6 + - - +
431D GLN* 3.2 9.8 + - - +
432D VAL* 3.0 32.9 + - - +
480D HEM 3.9 14.6 - - - -
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Residues in contact with LEU 429 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299D THR* 5.0 0.2 - - + -
336D MET* 5.9 0.4 - - + -
343D GLU* 4.2 13.9 - - + +
346D ALA* 3.8 28.9 - - + -
347D ARG* 3.9 29.4 - - + +
350D ILE* 4.7 6.5 - - + -
415D PHE* 4.1 28.5 - - + -
425D GLN* 3.0 24.7 + - + +
426D LYS* 4.0 6.3 - - + +
428D GLY* 1.3 71.8 - - - +
430D LEU* 1.3 57.6 + - - +
432D VAL* 4.3 8.5 - - + -
433D LYS* 2.8 51.2 + - + +
480D HEM 4.6 1.7 - - + +
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Residues in contact with LEU 430 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139D PHE* 3.6 22.7 - - + -
142D PHE* 3.6 33.2 - - + -
143D VAL* 3.6 28.3 - - + -
146D ILE* 3.8 11.2 - - + -
332D TYR* 4.8 0.2 - - + -
335D VAL* 3.8 14.4 - - + +
336D MET* 3.5 37.2 - - + +
426D LYS 2.9 17.3 + - - +
427D PHE* 3.2 10.7 + - + +
429D LEU* 1.3 73.1 - - - +
431D GLN* 1.3 61.7 + - - +
433D LYS* 4.7 0.2 - - - +
434D THR* 2.8 31.6 + - - +
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Residues in contact with GLN 431 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146D ILE* 4.1 26.2 - - + +
175D ILE* 3.6 24.7 - - + +
178D THR* 2.9 24.7 + - - +
179D ALA* 3.3 15.6 + - - +
292D GLY 5.1 0.6 + - - -
296D SER* 4.0 14.3 + - - -
427D PHE* 3.1 44.0 + - + +
428D GLY* 3.5 13.2 - - - +
430D LEU* 1.3 75.1 - - - +
432D VAL* 1.3 67.6 + - - +
434D THR* 3.3 2.3 + - - -
435D ILE* 3.0 28.9 + - + +
480D HEM 4.4 2.6 - - - +
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Residues in contact with VAL 432 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175D ILE* 4.9 0.2 - - - +
296D SER* 3.8 15.7 - - - +
299D THR* 3.9 20.6 - - + -
300D THR* 3.4 29.8 - - - +
303D SER* 4.6 0.9 - - - +
346D ALA* 3.6 27.8 - - + -
428D GLY 3.0 24.0 + - - +
429D LEU* 3.9 10.1 - - + +
431D GLN* 1.3 75.2 - - - +
433D LYS* 1.4 60.2 + - + +
435D ILE* 3.2 3.4 + - - +
436D LEU* 3.0 45.3 + - + +
480D HEM 5.0 1.3 - - + -
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Residues in contact with LYS 433 (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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335D VAL* 2.9 33.9 + - + +
336D MET* 3.9 20.2 + - - +
339D MET* 3.4 33.3 + - + +
342D ALA* 4.2 9.2 - - + +
343D GLU* 2.7 60.3 + - + +
346D ALA* 5.2 1.3 - - + -
429D LEU* 2.8 37.1 + - + +
432D VAL* 1.4 77.5 - - + +
434D THR* 1.3 62.9 + - - +
436D LEU* 3.5 6.3 + - - +
437D ALA* 3.0 19.6 + - - +
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Residues in contact with THR 434 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143D VAL* 4.6 9.2 - - + +
146D ILE* 3.7 29.3 - - + +
147D GLN* 4.0 27.8 - - + +
150D VAL* 5.1 1.3 - - + -
330D LEU* 4.4 7.9 - - + -
335D VAL* 3.7 20.8 - - - +
430D LEU* 2.8 25.7 + - - +
433D LYS* 1.3 75.7 - - - +
435D ILE* 1.3 55.4 + - - +
437D ALA* 3.5 4.3 + - - +
438D THR* 2.7 40.9 + - - +
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Residues in contact with ILE 435 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146D ILE* 5.3 0.9 - - + -
150D VAL* 3.7 25.8 - - + -
154D MET* 4.6 0.3 - - - +
171D CYS* 5.1 0.7 - - - +
174D MET* 4.3 35.2 - - + -
175D ILE* 3.5 36.3 - - + -
178D THR* 5.0 2.9 - - + +
300D THR* 3.5 30.7 - - + +
304D MET* 4.4 10.3 - - - -
431D GLN* 3.0 16.7 + - + +
432D VAL 3.6 5.6 - - - +
434D THR* 1.3 73.3 - - - +
436D LEU* 1.3 62.8 + - - +
438D THR* 3.3 3.7 + - - -
439D ALA* 2.8 33.7 + - + +
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Residues in contact with LEU 436 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300D THR* 4.2 6.7 - - + +
303D SER* 3.8 29.6 - - - -
304D MET* 3.5 32.3 - - + +
307D LEU* 4.5 15.0 - - + -
319D LEU* 4.6 11.9 - - + +
323D ILE* 4.4 0.5 - - - +
342D ALA* 4.3 21.8 - - + +
345D CYS* 4.8 3.4 - - + -
346D ALA* 4.9 0.7 - - + -
432D VAL* 3.0 33.1 + - + +
433D LYS* 3.8 7.2 - - - +
435D ILE* 1.3 78.1 - - - +
437D ALA* 1.3 56.4 + - - +
439D ALA* 4.7 1.1 - - - -
440D PHE* 3.1 40.0 + - + +
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Residues in contact with ALA 437 (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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323D ILE* 3.3 33.8 - - + +
326D PHE* 5.6 0.4 - - + -
330D LEU* 4.0 22.2 - - + -
339D MET* 4.0 10.2 - - + +
433D LYS 3.0 17.0 + - - +
434D THR 3.9 3.1 - - - +
436D LEU* 1.3 73.7 - - - +
438D THR* 1.3 61.0 + - - +
441D ARG* 2.9 33.0 + - - +
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Residues in contact with THR 438 (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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147D GLN* 3.5 28.8 + - + +
150D VAL* 3.7 27.5 - - + +
151D ARG* 4.0 34.0 + - + +
154D MET* 4.0 8.9 - - - +
330D LEU* 4.5 0.9 - - - +
434D THR* 2.7 24.2 + - - +
435D ILE 3.8 0.4 - - - -
437D ALA* 1.3 76.7 - - - +
439D ALA* 1.3 61.2 + - - +
441D ARG* 3.5 14.6 - - - +
442D SER* 3.7 12.4 + - - +
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Residues in contact with ALA 439 (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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154D MET* 3.4 23.2 - - + +
158D TRP* 4.3 0.9 - - + -
304D MET* 3.8 30.3 - - + -
435D ILE* 2.8 23.9 + - + +
436D LEU* 4.1 2.7 - - - +
438D THR* 1.3 73.8 - - - +
440D PHE* 1.3 60.4 + - + +
442D SER 3.2 1.7 + - - -
443D TYR* 2.8 35.6 + - - +
445D PHE* 4.1 5.8 - - + -
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Residues in contact with PHE 440 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304D MET* 3.9 32.1 - - + -
307D LEU* 3.7 35.9 - - + -
308D MET* 4.4 7.6 - - + -
316D LEU* 3.6 29.8 - - + -
319D LEU* 3.9 20.2 - - + -
320D ARG* 2.7 49.4 + - + +
323D ILE* 4.0 7.4 - - + -
436D LEU* 3.1 28.1 + - + +
439D ALA* 1.3 76.9 - - + +
441D ARG* 1.3 63.4 + - - +
442D SER 3.4 0.2 - - - -
443D TYR 3.5 5.8 - - - +
444D ASP* 5.2 0.4 - - - -
445D PHE* 3.6 27.8 - + - -
476D ARG* 3.9 0.3 + - - -
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Residues in contact with ARG 441 (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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151D ARG* 3.4 28.2 - - - +
320D ARG* 5.2 0.2 - - - +
323D ILE* 3.6 21.9 + - + +
324D GLU* 4.7 14.2 - - + +
326D PHE 4.4 9.5 + - - -
327D PRO 4.4 1.6 + - - -
328D ALA* 3.6 34.8 - - - +
437D ALA 2.9 23.3 + - - +
438D THR* 3.5 9.2 - - - +
440D PHE* 1.3 75.9 - - - +
442D SER* 1.3 68.8 + - - +
476D ARG* 3.2 22.0 + - - +
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Residues in contact with SER 442 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151D ARG* 5.3 4.3 + - - -
154D MET* 5.5 1.1 - - - -
438D THR* 3.9 10.0 + - - +
439D ALA 3.2 1.8 + - - -
441D ARG* 1.3 92.2 + - - +
443D TYR* 1.3 84.0 + - - +
475D ARG* 3.8 18.8 + - - -
476D ARG* 2.8 29.0 + - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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