Contacts of the helix formed by residues 424 - 442 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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134A LEU* 4.2 8.5 - - - -
422A CYS* 3.3 7.1 - - - -
423A ILE* 1.3 77.3 - - - +
425A GLN* 1.3 56.3 + - - +
426A LYS 3.3 2.5 - - - -
427A PHE* 3.1 5.7 + - - +
428A GLY* 2.8 31.0 + - - -
480A HEM 3.4 39.0 - - - +
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Residues in contact with GLN 425 (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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415A PHE* 3.5 56.9 + - + +
416A GLY 5.6 0.4 + - - -
421A LYS* 4.6 13.9 - - - +
422A CYS* 3.0 37.7 + - + +
423A ILE 3.4 2.0 + - - -
424A GLY* 1.3 76.1 - - - +
426A LYS* 1.3 68.6 + - + +
428A GLY* 3.5 1.0 + - - -
429A LEU* 3.1 32.6 + - + +
480A HEM 5.0 0.9 - - - -
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Residues in contact with LYS 426 (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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136A ILE* 4.6 15.7 - - + -
139A PHE* 3.8 18.0 - - + -
336A MET* 5.2 6.3 - - - +
343A GLU* 5.8 1.8 + - - -
423A ILE 5.1 1.4 + - - +
424A GLY 3.3 0.8 - - - -
425A GLN* 1.3 84.0 - - + +
427A PHE* 1.3 61.7 + - - +
429A LEU* 3.8 6.4 - - + +
430A LEU* 2.8 29.3 + - - +
409C GLU* 3.0 30.4 + - - +
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Residues in contact with PHE 427 (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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134A LEU* 4.2 16.4 - - + -
139A PHE* 3.7 17.5 - + + -
142A PHE* 3.4 39.5 - + - -
146A ILE* 4.8 2.0 - - + -
179A ALA* 4.1 13.0 - - + -
182A CYS* 3.8 23.6 - - + -
183A LEU* 4.2 22.2 - - + -
424A GLY 3.1 9.9 + - - +
426A LYS* 1.3 76.7 - - - +
428A GLY* 1.3 66.7 + - - +
430A LEU* 3.3 7.0 + - + +
431A GLN* 3.2 54.1 + - + +
480A HEM 3.8 24.0 - - + -
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Residues in contact with GLY 428 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296A SER* 3.7 21.5 + - - -
424A GLY 2.8 16.1 + - - -
425A GLN 3.9 1.3 - - - -
427A PHE* 1.3 77.0 - - - +
429A LEU* 1.3 56.4 + - - +
431A GLN* 3.2 11.1 + - - +
432A VAL* 3.0 32.5 + - - +
480A HEM 3.9 14.0 - - - +
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Residues in contact with LEU 429 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299A THR* 5.1 0.7 - - + -
343A GLU* 3.6 39.5 - - + +
346A ALA* 3.5 35.0 - - + -
347A ARG* 4.7 6.3 - - + +
350A ILE* 4.9 2.9 - - + -
415A PHE* 4.1 30.5 - - + -
425A GLN* 3.1 24.4 + - + +
426A LYS* 4.0 5.4 - - + +
428A GLY* 1.3 72.5 - - - +
430A LEU* 1.4 62.0 + - - +
432A VAL* 4.2 8.1 - - + -
433A LYS* 2.9 39.3 + - + +
480A HEM 4.7 1.3 - - + +
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Residues in contact with LEU 430 (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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139A PHE* 3.9 23.8 - - + -
142A PHE* 3.7 31.9 - - + -
143A VAL* 3.7 17.3 - - + -
146A ILE* 3.9 11.9 - - + -
335A VAL* 3.6 26.3 - - + +
336A MET* 3.0 30.1 - - + -
426A LYS 2.8 19.5 + - - +
427A PHE* 3.5 8.7 - - + +
428A GLY 3.2 0.2 - - - -
429A LEU* 1.4 76.9 - - - +
431A GLN* 1.3 59.3 + - - +
433A LYS* 5.0 2.2 - - - +
434A THR* 2.7 31.6 + - - +
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Residues in contact with GLN 431 (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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146A ILE* 3.8 27.6 - - + -
175A ILE* 3.7 21.9 - - + +
178A THR* 2.7 26.6 + - - +
179A ALA* 3.4 16.4 + - - +
292A GLY 5.3 0.6 + - - -
296A SER* 4.2 10.9 + - - -
427A PHE* 3.2 50.0 + - + +
428A GLY* 3.6 12.2 - - - +
430A LEU* 1.3 74.1 - - - +
432A VAL* 1.3 69.0 + - - +
434A THR* 3.4 1.0 + - - -
435A ILE* 3.0 31.1 + - + +
480A HEM 4.6 2.2 - - - +
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Residues in contact with VAL 432 (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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175A ILE* 5.4 0.2 - - + -
296A SER* 3.8 15.5 - - - +
299A THR* 4.0 16.8 - - + -
300A THR* 3.4 37.6 - - - +
303A SER* 4.6 2.5 - - - +
346A ALA* 3.9 23.8 - - + -
428A GLY 3.0 24.0 + - - +
429A LEU* 3.3 9.4 + - + +
431A GLN* 1.3 77.3 - - - +
433A LYS* 1.3 59.4 + - + +
435A ILE* 3.3 2.5 + - - +
436A LEU* 3.0 40.8 + - + +
480A HEM 5.2 1.6 - - + -
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Residues in contact with LYS 433 (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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335A VAL* 2.9 40.4 + - + -
336A MET* 4.0 15.6 + - - +
339A MET* 3.5 44.8 + - + +
340A PRO* 5.5 0.2 - - - +
342A ALA* 4.1 16.8 - - + +
343A GLU* 3.2 34.4 + - - +
429A LEU* 2.9 27.2 + - + +
430A LEU* 5.0 2.2 - - - +
432A VAL* 1.3 81.8 - - + +
434A THR* 1.3 57.2 + - - +
436A LEU* 3.7 5.2 - - - -
437A ALA* 2.9 31.7 + - - +
409C GLU* 5.4 1.4 + - - -
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Residues in contact with THR 434 (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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143A VAL* 4.1 8.0 - - + +
146A ILE* 3.6 31.8 - - + +
147A GLN* 3.8 28.9 - - + +
150A VAL* 5.1 0.9 - - + -
330A LEU* 4.2 11.4 - - + -
335A VAL* 3.7 17.0 - - - +
430A LEU* 2.7 25.9 + - - +
431A GLN 3.9 0.4 - - - -
433A LYS* 1.3 76.0 - - - +
435A ILE* 1.3 54.9 + - - +
437A ALA* 3.9 4.3 - - - +
438A THR* 2.6 39.0 + - - +
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Residues in contact with ILE 435 (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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146A ILE* 5.0 1.8 - - + -
150A VAL* 3.6 28.5 - - + -
154A MET* 4.6 0.6 - - + +
171A CYS* 5.2 0.4 - - - +
174A MET* 4.1 36.8 - - + -
175A ILE* 3.7 34.1 - - + +
178A THR* 5.0 3.1 - - + -
300A THR* 3.6 26.5 - - + +
304A MET* 4.5 9.2 - - - -
431A GLN* 3.0 23.0 + - + +
432A VAL 3.7 3.8 - - - +
434A THR* 1.3 73.6 - - - +
436A LEU* 1.3 60.3 + - - +
438A THR* 3.2 1.0 + - - -
439A ALA* 2.8 37.6 + - + +
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Residues in contact with LEU 436 (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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300A THR* 4.6 5.2 - - + +
303A SER* 4.0 22.4 - - - +
304A MET* 3.6 29.4 - - + -
307A LEU* 4.1 18.8 - - + -
319A LEU* 4.5 14.4 - - + +
339A MET* 5.2 1.1 - - + -
342A ALA* 4.4 28.5 - - + +
345A CYS* 4.9 2.0 - - + -
432A VAL* 3.0 36.8 + - + +
433A LYS* 3.3 4.2 + - - +
435A ILE* 1.3 77.4 - - - +
437A ALA* 1.3 57.3 + - - +
439A ALA* 4.7 1.1 - - - -
440A PHE* 3.0 41.1 + - + +
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Residues in contact with ALA 437 (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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319A LEU* 5.7 0.4 - - - -
323A ILE* 3.6 25.8 - - + +
326A PHE* 4.9 2.5 - - + -
330A LEU* 3.9 24.2 - - + -
339A MET* 3.8 19.4 - - + +
433A LYS 2.9 20.6 + - - +
434A THR 3.9 0.4 - - - +
436A LEU* 1.3 72.9 - - - +
438A THR* 1.3 58.6 + - - +
441A ARG* 3.1 29.6 + - - +
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Residues in contact with THR 438 (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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147A GLN* 3.2 30.2 + - + +
150A VAL* 3.7 26.5 - - + +
151A ARG* 3.9 36.2 + - + +
154A MET* 4.2 8.7 - - - +
330A LEU* 4.2 0.9 - - - +
434A THR* 2.6 25.3 + - - +
435A ILE 3.9 0.4 - - - -
437A ALA* 1.3 77.3 - - - +
439A ALA* 1.3 64.7 + - - +
441A ARG* 3.8 3.9 - - - +
442A SER* 3.5 20.7 + - - +
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Residues in contact with ALA 439 (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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154A MET* 3.6 23.3 - - + +
158A TRP* 4.3 0.7 - - + -
304A MET* 3.7 30.7 - - + -
435A ILE* 2.8 19.6 + - + +
436A LEU* 4.1 2.9 - - - +
438A THR* 1.3 76.3 - - - +
440A PHE* 1.4 59.0 + - + +
442A SER 3.2 2.8 + - - -
443A TYR* 2.8 34.4 + - - +
445A PHE* 4.1 7.0 - - + -
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Residues in contact with PHE 440 (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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304A MET* 4.0 36.6 - - + -
307A LEU* 3.8 32.8 - - + -
308A MET* 4.6 7.9 - - + -
316A LEU* 3.5 27.8 - - + -
319A LEU* 3.7 21.1 - - + -
320A ARG* 2.9 47.6 + - + +
323A ILE* 4.4 5.4 - - + -
436A LEU* 3.0 28.9 + - + +
439A ALA* 1.4 76.3 - - + +
441A ARG* 1.3 64.9 + - - +
442A SER 3.3 0.2 - - - -
443A TYR 3.5 8.3 - - - +
444A ASP* 5.4 0.4 - - - -
445A PHE* 3.5 27.6 - + + -
476A ARG* 3.8 0.9 + - - -
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Residues in contact with ARG 441 (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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147A GLN* 5.1 0.8 - - - +
151A ARG* 3.2 25.8 - - - +
323A ILE* 4.0 18.9 - - + +
324A GLU 6.0 0.2 + - - -
326A PHE* 4.5 10.4 + - - -
327A PRO 3.7 4.5 + - - -
328A ALA* 2.8 44.6 + - - +
330A LEU* 6.1 0.2 - - - +
437A ALA 3.1 23.2 + - - +
438A THR* 3.8 4.9 - - - +
440A PHE* 1.3 80.7 - - - +
442A SER* 1.3 65.4 + - - +
476A ARG* 3.6 14.9 + - - +
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Residues in contact with SER 442 (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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151A ARG* 5.1 7.6 + - - -
154A MET* 5.6 1.1 - - - -
438A THR* 3.5 9.6 + - - +
439A ALA 3.2 2.6 + - - -
441A ARG* 1.3 92.3 + - - +
443A TYR* 1.3 82.6 + - - +
475A ARG* 3.8 8.5 - - - +
476A ARG* 2.8 26.6 + - - +
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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
------------------------------------------------------------
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