Contacts of the helix formed by residues 411 - 426 (chain A) in PDB entry 6O0Z
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 PRO 411 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166A GLY* 4.5 0.4 - - - -
167A HIS* 3.6 24.9 - - + +
170A ILE* 4.9 13.0 - - + +
174A LEU* 4.5 14.8 - - + -
302A LEU* 5.8 4.7 - - + -
305A ILE* 5.5 8.5 - - + -
409A SER 3.3 9.6 - - - +
410A ILE* 1.3 101.1 - - + +
412A HIS* 1.3 64.3 - - - +
413A GLN* 3.3 18.1 + - - +
414A ILE* 3.5 24.5 + - + +
415A HIS* 3.9 2.8 - - - -
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Residues in contact with HIS 412 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165A ARG 3.2 26.5 - - - +
167A HIS 3.1 25.8 + - - +
168A PHE* 3.5 35.3 - + + -
170A ILE 4.9 1.5 + - - -
411A PRO* 1.3 71.8 - - - +
413A GLN* 1.3 95.8 + - + +
414A ILE 3.2 0.4 - - - -
415A HIS* 3.4 7.5 + - - +
416A LEU* 3.0 39.3 + - + +
444A LEU* 4.6 11.2 - - + +
445A THR* 3.9 21.6 + - - -
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Residues in contact with GLN 413 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170A ILE* 3.0 30.0 + - - +
171A GLU* 4.9 0.2 - - - +
172A GLY 3.4 18.3 + - - +
173A ASP* 5.0 1.6 - - - -
174A LEU* 4.1 44.3 - - + +
411A PRO* 3.2 21.6 - - + +
412A HIS* 1.3 105.5 + - + +
414A ILE* 1.3 61.3 + - + +
416A LEU* 3.6 10.3 - - + +
417A GLY* 2.9 25.3 + - - -
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Residues in contact with ILE 414 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174A LEU* 5.0 9.9 - - + +
176A PRO* 4.9 14.1 - - + -
302A LEU* 3.8 28.9 - - + -
316A PRO* 4.8 16.2 - - + -
317A LEU* 4.0 33.2 - - + -
410A ILE* 4.6 7.4 - - + -
411A PRO* 3.8 33.2 - - + +
412A HIS 3.2 0.4 - - - -
413A GLN* 1.3 75.9 - - - +
415A HIS* 1.3 60.8 + - - +
417A GLY* 3.3 2.2 + - - -
418A GLU* 3.0 32.4 + - + +
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Residues in contact with HIS 415 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136A TYR* 6.4 0.2 - + - -
139A ARG* 3.6 22.1 + - - +
161A MET* 3.4 28.9 - - + +
164A PHE* 4.4 10.8 + - + -
165A ARG* 3.7 28.0 - - - -
166A GLY* 3.8 9.4 + - - -
317A LEU* 3.9 22.4 - - + +
410A ILE* 3.6 17.7 - - + +
411A PRO 3.9 15.0 - - - -
412A HIS* 3.4 5.5 + - - +
414A ILE* 1.3 75.9 - - - +
416A LEU* 1.3 57.3 + - - +
418A GLU* 3.4 4.0 + - - -
419A LEU* 2.9 26.9 + - - +
444A LEU* 4.9 8.0 - - + +
19B G 5.5 0.6 + - - -
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Residues in contact with LEU 416 (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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412A HIS* 3.0 36.1 + - + +
413A GLN* 3.6 11.2 - - + +
414A ILE 3.2 0.2 - - - -
415A HIS* 1.3 77.7 - - - +
417A GLY* 1.3 56.7 + - - +
419A LEU* 3.4 10.9 + - + -
420A HIS* 2.9 32.5 + - + +
441A GLU* 4.6 24.2 - - + +
444A LEU* 4.1 19.9 - - + +
445A THR* 4.8 11.2 - - + +
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Residues in contact with GLY 417 (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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413A GLN 2.9 15.7 + - - -
414A ILE* 3.3 3.3 + - - -
416A LEU* 1.3 75.0 - - - +
418A GLU* 1.3 58.4 + - - +
420A HIS* 3.3 6.4 + - - +
421A ALA* 3.0 30.0 + - - +
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Residues in contact with GLU 418 (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 ARG* 2.5 42.5 + - - +
143A VAL* 4.0 8.0 - - + +
161A MET* 3.9 9.5 - - + +
314A LYS 5.7 0.2 - - - +
315A ALA* 3.6 27.9 - - + +
316A PRO* 5.4 1.3 - - + -
317A LEU* 3.5 23.0 + - - +
318A SER* 3.1 20.7 + - - -
414A ILE* 3.0 22.6 + - + +
415A HIS* 3.8 4.5 - - - +
417A GLY* 1.3 75.2 - - - +
419A LEU* 1.3 59.8 + - - +
421A ALA* 3.4 6.2 + - - +
422A ILE* 3.0 32.8 + - - +
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Residues in contact with LEU 419 (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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158A LEU* 3.7 26.2 - - + -
161A MET* 3.5 14.7 - - + -
162A ILE* 4.5 8.7 - - + -
415A HIS 2.9 19.1 + - - +
416A LEU* 3.8 13.2 - - + +
418A GLU* 1.3 76.5 - - - +
420A HIS* 1.3 59.7 + - - +
422A ILE* 3.7 4.9 - - - +
423A LEU* 2.9 53.3 + - + +
440A ILE* 4.3 17.3 - - + -
441A GLU* 4.5 18.4 - - + -
444A LEU* 3.7 24.9 - - + -
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Residues in contact with HIS 420 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416A LEU* 2.9 22.3 + - + +
417A GLY* 3.7 7.2 - - - +
418A GLU 3.3 0.2 - - - -
419A LEU* 1.3 80.4 - - + +
421A ALA* 1.3 58.5 + - - +
423A LEU* 3.8 6.7 - - - +
424A ARG* 2.9 55.3 + - + +
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Residues in contact with ALA 421 (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* 4.3 25.8 - - + +
314A LYS* 5.4 7.4 - - + -
417A GLY 3.0 17.4 + - - +
418A GLU* 3.8 4.3 - - - +
420A HIS* 1.3 76.0 - - - +
422A ILE* 1.3 60.8 + - - +
424A ARG* 3.3 7.7 + - - +
425A ARG* 3.0 38.3 + - - +
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Residues in contact with ILE 422 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139A ARG* 4.6 5.8 - - + +
142A LEU* 4.2 33.7 - - + -
143A VAL* 3.7 18.8 - - + -
154A ILE* 4.6 17.3 - - + -
157A ALA* 4.3 14.6 - - + -
158A LEU* 4.1 20.6 - - + -
161A MET* 4.0 23.8 - - + -
418A GLU 3.0 19.9 + - - +
419A LEU* 3.7 4.5 - - - +
421A ALA* 1.3 76.3 - - - +
423A LEU* 1.3 64.3 + - + +
425A ARG* 3.3 9.4 + - - +
426A GLN* 3.4 21.4 + - + +
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Residues in contact with LEU 423 (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 ILE* 5.7 1.6 - - + -
158A LEU* 4.2 21.1 - - + -
419A LEU* 2.9 42.2 + - + +
420A HIS* 3.9 7.6 - - - +
422A ILE* 1.3 79.8 - - + +
424A ARG* 1.3 62.5 + - - +
425A ARG 3.6 0.2 + - - -
426A GLN* 4.1 1.8 - - - -
427A GLU* 2.9 32.6 + - - +
433A LEU* 3.7 35.1 - - + +
436A ASN 5.2 0.4 - - - +
437A ARG 4.1 24.9 - - - +
440A ILE* 4.3 13.0 - - + -
441A GLU* 5.8 0.7 - - + -
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Residues in contact with ARG 424 (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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420A HIS* 2.9 43.6 + - + +
421A ALA* 3.7 8.1 - - - +
422A ILE 3.2 0.2 - - - -
423A LEU* 1.3 78.4 - - - +
425A ARG* 1.3 62.7 + - - +
427A GLU* 3.5 19.9 - - + +
428A ASP* 5.5 0.2 - - - +
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Residues in contact with ARG 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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142A LEU 4.3 10.5 - - - +
143A VAL* 3.2 18.0 + - - +
144A ASP* 2.9 29.1 + - - +
145A SER 3.6 17.5 - - - +
146A THR* 3.5 27.6 - - - +
314A LYS* 5.5 8.9 - - - +
421A ALA* 3.0 24.5 + - - +
422A ILE 3.3 3.5 + - - +
424A ARG* 1.3 81.6 - - - +
426A GLN* 1.3 64.6 + - + +
427A GLU 3.3 2.6 + - - -
428A ASP* 4.1 8.8 - - - +
429A PHE* 4.1 10.0 - - - -
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Residues in contact with GLN 426 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142A LEU* 4.3 18.5 - - + +
145A SER 4.6 9.0 - - - +
146A THR 5.3 0.5 - - - -
147A ASP 3.0 20.8 + - - +
148A LYS* 3.8 6.7 - - - +
149A ALA* 3.5 26.7 + - - +
154A ILE* 4.5 23.4 - - + +
422A ILE* 3.4 17.6 + - + +
423A LEU* 4.1 3.4 - - - +
424A ARG 3.5 0.2 - - - -
425A ARG* 1.3 81.7 - - + +
427A GLU* 1.3 64.5 + - - +
428A ASP 3.6 1.1 - - - -
429A PHE* 3.9 18.0 + - - -
430A TYR* 4.0 24.6 + - + -
433A LEU* 4.4 12.4 - - + +
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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