Contacts of the helix formed by residues 424 - 442 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134B LEU* 4.3 5.2 - - - -
422B CYS* 3.3 7.0 - - - -
423B ILE* 1.3 82.3 - - - +
425B GLN* 1.3 64.7 + - - +
426B LYS 3.3 2.9 - - - -
427B PHE* 3.1 7.8 + - - +
428B GLY* 2.9 21.3 + - - -
480B HEM 3.4 37.4 - - - +
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Residues in contact with GLN 425 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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343B GLU* 5.4 0.5 - - - +
347B ARG* 3.6 17.8 + - - -
415B PHE* 3.5 58.0 + - + +
421B LYS* 6.3 1.2 - - - +
422B CYS* 3.2 23.0 + - - +
423B ILE 3.4 2.4 - - - -
424B GLY* 1.3 74.3 - - - +
426B LYS* 1.3 66.6 + - + +
428B GLY* 3.5 0.7 + - - -
429B LEU* 3.0 42.3 + - + +
480B HEM 5.0 0.9 - - - -
338D GLU* 4.5 25.2 + - - +
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Residues in contact with LYS 426 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134B LEU 5.7 0.7 - - - +
136B ILE* 5.5 4.3 - - + -
139B PHE* 3.7 20.9 - - + -
336B MET* 5.1 2.5 - - - +
423B ILE 5.0 1.2 + - - -
424B GLY 3.3 0.8 - - - -
425B GLN* 1.3 86.7 + - + +
427B PHE* 1.3 58.8 + - - +
429B LEU* 3.5 5.4 + - + +
430B LEU* 2.9 28.9 + - - +
325D GLU* 3.4 44.0 - - + +
326D PHE* 4.4 10.5 - - - -
334D ASN* 4.6 2.8 + - - -
338D GLU* 2.6 31.4 + - - -
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Residues in contact with PHE 427 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134B LEU* 4.4 19.5 - - + -
139B PHE* 3.7 16.6 - + + -
142B PHE* 3.6 40.2 - + - -
146B ILE* 4.8 1.8 - - + -
179B ALA* 4.0 13.9 - - + -
182B CYS* 3.9 23.3 - - + -
183B LEU* 3.9 21.1 - - + -
424B GLY* 3.1 10.3 + - - +
426B LYS* 1.3 76.5 - - - +
428B GLY* 1.3 66.3 + - - +
430B LEU* 3.5 4.1 + - + +
431B GLN* 3.2 52.8 + - + +
480B HEM 4.1 22.2 - - + -
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Residues in contact with GLY 428 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296B SER* 3.6 22.3 + - - -
424B GLY 2.9 14.3 + - - -
425B GLN 3.9 1.1 - - - -
427B PHE* 1.3 77.4 - - - +
429B LEU* 1.3 56.8 + - - +
431B GLN* 3.1 11.6 + - - +
432B VAL* 3.0 32.1 + - - +
480B HEM 3.9 14.0 - - - +
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Residues in contact with LEU 429 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299B THR* 4.8 0.7 - - + -
343B GLU* 3.7 29.4 - - + +
346B ALA* 3.8 29.6 - - + -
347B ARG* 4.6 5.6 - - + +
350B ILE* 4.7 5.4 - - + -
415B PHE* 4.0 24.2 - - + -
425B GLN* 3.0 43.4 + - + +
426B LYS* 4.1 5.2 - - + +
428B GLY* 1.3 73.7 - - - +
430B LEU* 1.3 60.4 + - - +
432B VAL* 3.7 8.7 - - + +
433B LYS* 2.9 48.4 + - + +
480B HEM 5.1 1.6 - - + -
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Residues in contact with LEU 430 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139B PHE* 3.6 31.0 - - + -
142B PHE* 3.7 16.8 - - + -
143B VAL* 3.4 25.1 - - + -
146B ILE* 3.7 24.9 - - + -
335B VAL* 3.8 8.0 - - + +
336B MET* 2.5 40.8 - - + +
426B LYS 2.9 18.5 + - - +
427B PHE* 3.6 6.7 - - + +
428B GLY 3.3 0.2 - - - -
429B LEU* 1.3 76.4 - - - +
431B GLN* 1.3 62.0 + - - +
433B LYS* 4.0 0.9 - - - +
434B THR* 2.8 30.8 + - - +
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Residues in contact with GLN 431 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146B ILE* 4.0 25.4 - - + +
175B ILE* 3.6 24.4 - - + +
178B THR* 2.6 27.9 + - - +
179B ALA* 3.2 18.2 + - - +
292B GLY 5.1 0.8 + - - -
296B SER* 4.1 10.3 + - - -
427B PHE* 3.2 42.6 + - + +
428B GLY* 3.1 14.3 + - - +
430B LEU* 1.3 80.8 - - - +
432B VAL* 1.3 63.3 + - - +
434B THR* 3.4 1.7 + - - -
435B ILE* 3.0 30.1 + - - +
480B HEM 4.8 1.8 - - - +
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Residues in contact with VAL 432 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296B SER* 3.8 15.9 - - - +
299B THR* 3.9 18.4 - - + +
300B THR* 3.4 37.2 - - - +
303B SER* 4.8 0.9 - - - +
346B ALA* 3.9 24.7 - - + -
428B GLY 3.0 21.7 + - - +
429B LEU* 3.7 11.0 - - + +
431B GLN* 1.3 75.5 - - - +
433B LYS* 1.3 60.6 + - + +
435B ILE* 3.3 4.5 + - - +
436B LEU* 3.0 40.9 + - + +
480B HEM 5.2 0.9 - - + -
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Residues in contact with LYS 433 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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335B VAL* 2.9 40.7 + - + -
336B MET* 4.7 12.6 + - - +
339B MET* 3.3 36.9 + - + +
342B ALA* 4.2 13.2 - - + +
343B GLU* 3.0 51.4 + - + +
346B ALA* 5.5 1.6 - - + -
429B LEU* 2.9 30.2 + - + +
432B VAL* 1.3 78.0 - - + +
434B THR* 1.3 63.0 + - - +
436B LEU* 3.8 5.3 - - + +
437B ALA* 3.0 20.6 + - - +
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Residues in contact with THR 434 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143B VAL* 4.2 7.6 - - + +
146B ILE* 3.4 32.9 - - + +
147B GLN* 3.8 28.5 - - + +
150B VAL* 5.0 1.1 - - + -
330B LEU* 4.1 15.3 - - + -
335B VAL* 3.8 17.5 - - - +
430B LEU* 2.8 27.6 + - - +
431B GLN 3.8 0.2 - - - -
433B LYS* 1.3 75.4 - - - +
435B ILE* 1.3 56.3 + - - +
437B ALA* 4.0 0.7 - - - +
438B THR* 2.6 37.5 + - - +
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Residues in contact with ILE 435 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150B VAL* 3.7 25.6 - - + -
154B MET* 4.6 0.7 - - + +
171B CYS 5.1 0.7 - - - +
174B MET* 4.0 37.2 - - + -
175B ILE* 3.8 30.5 - - + +
178B THR* 5.1 2.9 - - + -
300B THR* 3.5 30.5 - - + +
304B MET* 4.5 10.1 - - - -
431B GLN* 3.0 20.4 + - + +
432B VAL 3.3 6.7 + - - +
434B THR* 1.3 76.4 - - - +
436B LEU* 1.3 53.4 + - - +
438B THR* 3.3 4.5 + - - -
439B ALA* 2.8 36.2 + - + +
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Residues in contact with LEU 436 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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300B THR* 4.4 6.5 - - + +
303B SER* 4.0 24.9 - - - -
304B MET* 3.7 29.6 - - + +
307B LEU* 4.4 10.3 - - + -
319B LEU* 4.6 12.6 - - + -
339B MET* 5.0 3.6 - - + -
342B ALA* 4.2 28.3 - - + +
345B CYS* 4.8 2.7 - - + -
346B ALA 5.1 0.4 - - - +
432B VAL* 3.0 34.6 + - + +
433B LYS* 3.8 4.9 - - + +
435B ILE* 1.3 76.9 - - - +
437B ALA* 1.3 57.9 + - - +
439B ALA* 4.7 1.3 - - - -
440B PHE* 3.0 48.0 + - + +
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Residues in contact with ALA 437 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147B GLN* 5.3 0.9 - - - -
319B LEU* 5.7 0.7 - - - -
323B ILE* 3.9 19.3 - - + +
326B PHE* 4.8 0.9 - - + -
330B LEU* 3.8 27.6 - - + -
339B MET* 3.6 19.9 - - + +
433B LYS 3.0 17.6 + - - +
436B LEU* 1.3 77.1 - - - +
438B THR* 1.3 59.3 + - - +
441B ARG* 3.0 34.3 + - + +
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Residues in contact with THR 438 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147B GLN* 3.0 36.5 + - + +
150B VAL* 3.8 24.7 - - + -
151B ARG* 3.8 30.3 + - + +
154B MET* 4.1 7.6 - - - +
330B LEU* 4.2 0.5 - - - +
434B THR* 2.6 24.9 + - - +
435B ILE 3.8 2.5 - - - -
437B ALA* 1.3 77.1 - - - +
439B ALA* 1.3 66.9 + - - +
440B PHE 3.5 0.2 + - - -
441B ARG* 3.6 9.3 + - - +
442B SER* 3.6 15.1 + - - -
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Residues in contact with ALA 439 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154B MET* 3.5 24.4 - - + +
158B TRP* 4.4 0.4 - - + -
304B MET* 3.9 30.1 - - + -
435B ILE* 2.8 22.8 + - + +
436B LEU* 4.0 3.4 - - - +
438B THR* 1.3 73.1 - - - +
440B PHE* 1.3 61.1 + - + +
442B SER 3.2 2.6 + - - -
443B TYR* 2.9 34.8 + - - +
445B PHE* 4.0 7.6 - - + -
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Residues in contact with PHE 440 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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304B MET* 4.0 33.4 - - + -
307B LEU* 3.5 39.3 - - + -
308B MET* 4.6 7.2 - - + -
316B LEU* 3.6 26.7 - - + -
319B LEU* 3.7 20.2 - - + -
320B ARG* 2.8 47.1 + - + +
323B ILE* 4.4 7.9 - - + -
436B LEU* 3.0 28.9 + - + +
439B ALA* 1.3 77.7 - - + +
441B ARG* 1.3 64.4 + - - +
443B TYR 3.4 2.9 - - - +
444B ASP* 5.2 0.9 - - - -
445B PHE* 3.5 31.4 - + - -
476B ARG* 4.0 0.7 + - - -
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Residues in contact with ARG 441 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147B GLN* 6.2 0.4 - - - +
151B ARG* 4.9 12.1 - - - +
320B ARG* 6.0 0.2 - - - +
323B ILE* 3.8 29.3 + - + +
324B GLU* 4.8 5.5 + - - +
326B PHE* 2.8 32.3 + - + +
327B PRO 3.6 4.9 + - - -
328B ALA* 3.3 33.8 - - - +
330B LEU* 6.5 0.7 - - + -
437B ALA* 3.0 27.3 + - + +
438B THR* 3.7 7.9 - - - +
439B ALA 3.2 0.2 - - - -
440B PHE* 1.3 78.8 - - - +
442B SER* 1.3 62.8 + - - +
476B ARG* 3.2 25.2 + - - +
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Residues in contact with SER 442 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151B ARG* 5.4 7.1 + - - -
154B MET* 4.9 1.6 - - - -
438B THR 3.6 9.2 + - - -
439B ALA 3.2 2.2 + - - -
441B ARG* 1.3 85.5 - - - +
443B TYR* 1.3 84.5 + - - +
475B ARG* 3.4 21.3 + - - -
476B ARG* 2.9 36.3 + - - +
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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
------------------------------------------------------------
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