Contacts of the helix formed by residues 533 - 550 (chain B) in PDB entry 1M2V
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 ASN 533 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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530B SER* 3.0 6.1 + - - +
531B GLY 2.9 5.7 - - - +
532B LYS* 1.3 78.1 - - + +
534B PRO* 1.3 59.0 - - - +
535B ASN* 2.8 41.3 + - - +
536B ASP* 3.1 61.4 + - - +
537B ILE* 3.9 4.0 + - - +
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Residues in contact with PRO 534 (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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531B GLY 4.1 5.4 - - - +
532B LYS 3.6 9.4 - - - +
533B ASN* 1.3 86.5 - - - +
535B ASN* 1.3 65.4 + - - +
537B ILE* 4.1 13.1 - - + +
538B VAL* 2.9 23.6 + - - +
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Residues in contact with ASN 535 (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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533B ASN* 2.8 26.8 + - - +
534B PRO* 1.3 86.9 - - - +
536B ASP* 1.3 66.4 + - - +
537B ILE 3.0 2.2 - - - -
538B VAL* 2.8 23.1 + - + +
539B LYS* 2.9 14.1 + - - +
868B TYR* 5.3 2.1 - - + -
870B SER* 4.9 10.3 + - - +
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Residues in contact with ASP 536 (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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526B TYR* 5.5 0.3 - - - -
527B PRO 4.7 3.1 - - - +
528B GLY 3.3 22.5 - - - +
529B PHE* 3.5 24.0 - - + -
530B SER* 2.9 30.1 + - - +
533B ASN* 3.1 31.4 + - - +
535B ASN* 1.3 73.9 - - - +
537B ILE* 1.3 64.0 + - + +
539B LYS* 3.4 5.0 + - - +
540B PHE* 3.1 27.0 + - - +
870B SER* 5.7 1.3 - - - -
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Residues in contact with ILE 537 (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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320B GLY* 6.5 0.7 - - - -
324B THR* 3.9 31.4 - - + +
529B PHE* 4.3 11.2 - - + -
531B GLY* 4.1 33.0 - - - +
533B ASN 4.3 4.5 - - - +
534B PRO* 4.1 12.3 - - + +
535B ASN 3.0 0.2 - - - -
536B ASP* 1.3 78.1 - - - +
538B VAL* 1.3 57.8 + - + +
541B SER* 2.8 39.1 + - - -
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Residues in contact with VAL 538 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
534B PRO 2.9 22.9 - - - +
535B ASN* 2.8 22.1 + - - +
537B ILE* 1.3 71.4 - - + +
539B LYS* 1.3 66.2 + - - +
541B SER* 4.6 2.2 - - - -
542B THR* 2.7 38.7 + - - +
868B TYR* 4.1 24.7 - - + +
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Residues in contact with LYS 539 (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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525B PHE 5.8 2.0 - - - -
526B TYR* 4.1 15.9 - - + +
535B ASN 2.9 10.1 + - - +
536B ASP* 3.9 8.5 - - - +
538B VAL* 1.3 79.8 - - - +
540B PHE* 1.3 67.0 + - - +
542B THR* 3.4 0.9 - - - -
543B GLU* 2.8 52.3 + - - +
806B ASN* 3.5 22.4 + - - +
807B GLU* 5.0 5.3 + - - +
867B THR* 5.7 1.6 - - - +
868B TYR* 3.1 37.3 + - + +
870B SER* 3.6 25.1 - - - +
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Residues in contact with PHE 540 (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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321B LEU* 3.8 24.9 - - + -
324B THR* 3.9 18.8 - - + -
325B THR* 3.7 22.4 - - - -
328B THR* 5.3 0.2 - - - -
445B VAL* 3.9 9.4 - - + -
500B PHE* 3.7 28.7 - + + -
502B ALA* 4.0 12.6 - - + -
526B TYR* 3.6 36.1 - + + -
529B PHE* 3.7 13.5 - + + -
536B ASP 3.1 14.9 + - - +
537B ILE 4.2 0.4 - - - +
539B LYS* 1.3 79.7 - - - +
541B SER* 1.3 58.1 - - - +
543B GLU* 3.2 0.7 + - - +
544B PHE* 2.8 59.7 + + + +
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Residues in contact with SER 541 (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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324B THR* 3.7 11.1 - - - +
328B THR* 2.9 33.3 + - - +
537B ILE* 2.8 28.4 + - - -
538B VAL* 4.2 2.7 - - - -
540B PHE* 1.3 78.8 - - - +
542B THR* 1.3 57.5 + - - +
544B PHE* 4.5 0.4 - - - -
545B ALA* 3.0 29.1 + - - +
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Residues in contact with THR 542 (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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538B VAL* 2.7 34.1 + - - +
539B LYS 2.9 3.6 + - - -
541B SER* 1.3 74.6 - - - +
543B GLU* 1.3 66.6 + - - +
545B ALA* 3.2 6.8 + - - +
546B LYS* 3.0 41.2 + - + +
866B ILE 4.9 0.2 - - - +
867B THR 5.5 0.2 - - - +
868B TYR* 3.8 28.0 - - + -
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Residues in contact with GLU 543 (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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524B HIS* 4.4 5.7 + - - -
526B TYR* 2.6 41.4 + - + +
539B LYS* 2.8 50.8 + - - +
540B PHE 3.7 1.1 - - - +
542B THR* 1.3 73.9 - - - +
544B PHE* 1.3 58.0 + - - +
546B LYS* 3.0 4.9 + - - +
547B HIS* 2.8 28.6 + - - +
866B ILE* 3.6 30.3 - - + +
867B THR* 4.1 8.2 - - - +
868B TYR* 3.2 28.5 + - + +
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Residues in contact with PHE 544 (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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308B PHE* 3.9 27.4 - + - -
325B THR* 4.2 21.8 - - + -
328B THR* 3.7 21.1 - - + -
329B LEU* 4.5 12.3 - - + -
443B ILE* 3.9 17.3 - - + -
445B VAL* 3.6 27.6 - - + -
500B PHE* 3.7 32.4 - + + -
540B PHE* 2.8 38.3 + + + +
541B SER 4.1 2.5 - - - +
543B GLU* 1.3 73.0 - - - +
545B ALA* 1.3 63.1 + - - +
547B HIS* 3.3 1.0 + - - +
548B ILE* 3.2 38.2 + - + +
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Residues in contact with ALA 545 (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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328B THR* 3.9 6.7 - - + +
332B ASN* 3.4 28.7 - - - +
335B SER* 5.1 2.0 - - - -
541B SER 3.0 21.9 + - - +
542B THR* 3.3 7.9 - - - +
543B GLU 3.1 0.2 - - - -
544B PHE* 1.3 77.4 - - - +
546B LYS* 1.3 64.0 + - + +
548B ILE* 3.2 10.2 - - - +
549B SER* 3.2 22.3 + - - -
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Residues in contact with LYS 546 (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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213B LEU* 4.3 5.5 - - + +
214B TYR* 4.2 14.7 + - + +
542B THR* 3.0 30.5 + - + +
543B GLU 3.4 6.3 - - - +
545B ALA* 1.3 76.2 - - + +
547B HIS* 1.3 62.1 + - - +
549B SER* 2.7 22.0 + - - -
550B MET* 3.0 14.0 + - - +
860B ARG 4.7 2.7 + - - -
861B ASN* 4.7 5.4 + - - +
862B HIS* 2.5 41.2 + - - +
865B VAL 3.6 12.7 + - - +
866B ILE* 3.6 35.1 - - + +
867B THR 4.4 4.2 + - - -
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Residues in contact with HIS 547 (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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441B LYS* 3.4 24.2 + - - -
443B ILE* 4.2 13.7 - - + -
498B ASP* 2.9 41.8 + - + +
500B PHE* 3.6 34.8 - + + -
522B GLN* 5.2 4.3 - - + -
524B HIS* 4.2 15.7 + - - -
543B GLU 2.8 15.4 + - - +
544B PHE 3.7 2.9 - - - +
545B ALA 3.2 0.2 - - - -
546B LYS* 1.3 76.4 - - - +
548B ILE* 1.3 62.5 + - + +
549B SER 3.6 0.2 + - - -
550B MET* 3.6 32.2 - - + +
589B PRO* 6.4 1.3 - - + -
591B ASP* 5.4 1.5 + - - -
866B ILE* 3.6 12.8 - - + +
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Residues in contact with ILE 548 (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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306B TYR* 3.8 14.3 + - + -
308B PHE* 4.0 24.2 - - + -
329B LEU* 4.1 16.6 - - + -
332B ASN* 3.8 25.8 - - + +
336B ILE* 3.6 36.6 - - + +
337B PRO* 3.2 21.0 - - - +
443B ILE* 4.2 11.0 - - + -
544B PHE* 3.2 28.6 + - + +
545B ALA* 3.2 16.4 - - - +
547B HIS* 1.3 76.5 - - + +
549B SER* 1.3 59.4 + - - +
550B MET 3.3 1.0 - - - +
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Residues in contact with SER 549 (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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214B TYR* 3.2 37.8 + - - -
335B SER* 3.4 37.6 - - - +
337B PRO* 3.7 10.2 - - - +
545B ALA 3.2 14.2 + - - -
546B LYS* 2.7 21.8 + - - -
548B ILE* 1.3 75.5 - - - +
550B MET* 1.3 66.5 + - - +
551B ASP* 3.7 2.1 + - - +
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Residues in contact with MET 550 (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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213B LEU* 3.6 27.4 - - + +
214B TYR* 4.8 0.2 - - - -
306B TYR* 4.3 4.9 + - - -
337B PRO* 3.5 10.3 - - - +
441B LYS* 5.5 4.3 - - - +
546B LYS 3.0 10.1 + - - +
547B HIS* 3.6 37.9 - - + +
548B ILE 3.3 4.8 - - - +
549B SER* 1.3 81.7 - - - +
551B ASP* 1.3 72.4 + - - +
552B PHE* 4.4 5.9 - - - -
589B PRO* 4.0 7.4 - - + -
590B ARG* 3.4 33.0 - - + -
591B ASP* 3.2 30.5 - - + +
866B ILE* 4.0 13.9 - - + -
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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