Contacts of the helix formed by residues 482 - 495 (chain B) in PDB entry 1M7X
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 482 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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480B LYS 3.5 1.4 + - - -
481B TRP* 1.3 67.6 - - - +
483B LEU* 1.3 65.3 + - - +
484B GLY 3.9 2.3 + - - -
485B TRP* 3.2 24.8 + - + +
486B MET 3.2 15.1 + - - -
510B GLY* 5.3 2.6 + - - -
513B TYR* 2.7 32.6 + - - -
514B ASN* 5.1 3.6 - - - +
519B PHE* 3.3 44.8 - - + +
520B VAL 2.8 21.0 + - - +
521B LEU* 3.9 12.2 - - + +
522B PRO* 3.5 12.2 - - + +
560B PHE* 5.5 2.2 - - - -
561B PRO 5.5 0.4 + - - -
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Residues in contact with LEU 483 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
458B GLU* 4.0 22.2 - - + +
459B GLU 4.2 5.8 - - - +
460B SER* 4.0 31.0 - - - +
480B LYS* 5.9 0.4 - - - +
481B TRP* 3.0 36.8 + - + +
482B ASN* 1.3 72.1 - - - +
484B GLY* 1.3 65.2 + - - +
486B MET* 2.9 25.2 + - + +
487B HIS* 2.8 40.5 + - + +
522B PRO* 4.9 4.0 - - + -
524B SER* 6.2 0.2 - - - +
527B GLU* 5.2 2.7 - - - +
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Residues in contact with GLY 484 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
482B ASN* 3.3 2.8 + - - -
483B LEU* 1.3 78.3 - - - +
485B TRP* 1.3 56.3 + - - +
487B HIS* 3.3 9.5 + - - +
488B ASP* 2.8 37.1 + - - +
513B TYR* 3.6 12.3 - - - -
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Residues in contact with TRP 485 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
482B ASN* 3.2 27.2 + - - +
483B LEU 3.1 0.6 - - - -
484B GLY* 1.3 70.8 - - - +
486B MET* 1.3 79.4 + - + +
488B ASP* 4.5 4.9 - - - +
489B THR* 2.7 64.8 + - + +
506B LYS 5.9 0.2 - - - -
510B GLY* 4.9 6.1 - - - -
513B TYR* 3.1 10.3 + - - +
521B LEU* 3.9 31.2 - - + -
522B PRO 4.5 1.6 - - - -
523B LEU* 3.9 16.6 - - + -
553B TYR* 3.5 27.6 - + - -
556B TRP* 4.3 7.1 - + - +
557B MET* 3.4 43.7 - - + -
560B PHE* 3.3 41.4 - + - -
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Residues in contact with MET 486 (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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482B ASN 3.2 9.0 + - - +
483B LEU* 2.9 26.1 + - + +
485B TRP* 1.3 89.5 - - + +
487B HIS* 1.3 93.4 + - + +
489B THR* 3.7 1.4 + - - -
490B LEU* 3.1 52.9 + - + +
522B PRO* 3.3 28.3 - - + +
523B LEU* 4.3 3.8 - - + -
527B GLU* 3.4 41.5 - - + +
553B TYR* 5.0 0.2 - - - -
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Residues in contact with HIS 487 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
483B LEU* 2.8 32.9 + - + +
484B GLY* 3.6 9.8 - - - +
486B MET* 1.3 103.3 - - + +
488B ASP* 1.3 61.2 + - - +
490B LEU* 4.0 1.8 - - - +
491B ASP* 3.1 40.1 + - - +
527B GLU* 4.8 4.7 + - - -
532B LYS* 5.8 2.6 + - - -
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Residues in contact with ASP 488 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
484B GLY* 2.8 25.3 + - - +
485B TRP* 3.9 4.9 - - - +
487B HIS* 1.3 77.9 - - - +
489B THR* 1.3 57.2 + - + +
491B ASP* 3.4 6.3 + - - +
492B TYR 3.1 21.1 + - - -
506B LYS* 3.4 51.7 + - - +
509B PHE* 4.0 25.8 - - - +
510B GLY 5.5 0.5 + - - -
513B TYR* 5.3 2.3 + - - -
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Residues in contact with THR 489 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
485B TRP* 2.7 66.5 + - + +
486B MET 3.7 1.4 + - - -
488B ASP* 1.3 69.9 - - - +
490B LEU* 1.3 59.9 + - - +
492B TYR* 3.3 1.9 + - - +
493B MET* 2.9 35.3 + - - +
506B LYS 4.0 11.7 - - - +
507B LEU* 4.1 19.1 - - + -
553B TYR* 2.8 33.1 + - + -
556B TRP* 4.4 7.6 - - + +
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Residues in contact with LEU 490 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
486B MET* 3.1 45.6 + - + +
487B HIS* 4.1 3.1 - - - +
489B THR* 1.3 76.3 + - - +
491B ASP* 1.3 60.5 + - - +
493B MET* 3.5 4.2 + - + +
494B LYS* 2.9 37.1 + - - +
523B LEU* 4.7 5.6 - - + -
527B GLU* 4.8 3.1 - - + -
535B ILE* 4.5 18.2 - - + -
538B ARG* 3.8 38.5 - - - +
539B MET* 5.2 2.6 - - + +
553B TYR* 3.1 41.7 - - + +
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Residues in contact with ASP 491 (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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487B HIS* 3.1 29.2 + - - +
488B ASP* 3.6 6.6 - - - +
490B LEU* 1.3 74.5 - - - +
492B TYR* 1.3 66.3 + - - +
494B LYS* 3.3 27.2 + - - +
495B LEU* 3.2 26.7 + - - +
506B LYS* 4.0 26.5 + - + +
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Residues in contact with TYR 492 (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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488B ASP 3.1 11.0 + - - +
489B THR 3.5 5.2 - - - +
491B ASP* 1.3 76.5 - - - +
493B MET* 1.3 73.4 + - - +
495B LEU* 3.0 27.7 + - - +
500B ARG* 3.1 56.8 + - + +
503B HIS* 3.4 26.5 - - + -
504B HIS* 4.3 7.9 - + - -
506B LYS* 4.0 4.6 - - + +
507B LEU* 3.3 50.3 - - + +
637B SER* 3.6 24.6 + - - -
639B LEU* 4.3 4.0 - - - +
657B PHE* 3.6 25.7 - + - +
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Residues in contact with MET 493 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
489B THR 2.9 20.7 + - - +
490B LEU* 3.9 4.7 - - - +
492B TYR* 1.3 85.4 - - - +
494B LYS* 1.3 62.3 + - - +
500B ARG* 3.0 21.9 + - - +
507B LEU* 5.9 1.3 - - - -
539B MET* 3.6 27.1 - - + +
540B PRO* 3.2 14.3 - - - +
549B ASN* 3.4 46.2 - - - +
552B ALA* 5.5 0.2 - - + -
553B TYR* 3.7 37.9 - - + -
657B PHE* 4.0 23.3 - - + -
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Residues in contact with LYS 494 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
490B LEU* 2.9 23.5 + - - +
491B ASP* 3.7 28.4 + - - +
492B TYR 3.2 0.4 - - - -
493B MET* 1.3 75.9 - - - +
495B LEU* 1.3 62.2 + - - +
496B ASP 3.6 1.6 + - - -
538B ARG* 3.3 51.8 - - + +
540B PRO* 4.3 9.0 - - - +
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Residues in contact with LEU 495 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
491B ASP 3.2 19.0 + - - +
492B TYR* 3.0 21.3 + - - +
493B MET 3.5 0.3 - - - +
494B LYS* 1.3 77.5 - - - +
496B ASP* 1.3 63.4 + - - +
497B PRO 3.3 0.2 - - - -
499B TYR* 4.4 11.4 - - + -
500B ARG* 2.5 49.3 + - + +
503B HIS* 3.3 52.5 - - + +
506B LYS* 4.8 3.1 - - + -
540B PRO* 3.6 2.5 - - - +
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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