Contacts of the helix formed by residues 482 - 495 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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480D LYS 3.6 0.4 + - - -
481D TRP* 1.3 72.4 - - - +
483D LEU* 1.3 62.9 + - - +
484D GLY* 3.7 3.1 + - - -
485D TRP* 3.3 25.4 + - + +
486D MET* 3.2 14.4 + - - +
510D GLY* 5.4 2.2 + - - -
513D TYR* 3.0 32.5 + - - -
514D ASN* 5.6 2.8 - - - +
519D PHE* 3.3 43.8 - - + +
520D VAL 2.9 17.6 + - - +
521D LEU* 4.1 10.6 - - + +
522D PRO* 3.3 14.4 - - - +
560D PHE* 5.8 2.0 - - - -
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Residues in contact with LEU 483 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
458D GLU* 3.9 37.5 - - + +
459D GLU 4.4 4.7 - - - +
460D SER* 4.0 24.0 - - - +
480D LYS* 5.9 1.3 - - - +
481D TRP* 3.4 25.1 + - + +
482D ASN* 1.3 71.8 - - - +
484D GLY* 1.3 55.5 + - - +
486D MET* 3.0 21.8 + - + +
487D HIS* 2.7 55.4 + - + -
522D PRO* 4.8 3.6 - - + -
527D GLU* 5.1 4.0 - - - +
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Residues in contact with GLY 484 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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482D ASN* 3.3 2.8 + - - -
483D LEU* 1.3 79.9 - - - +
485D TRP* 1.3 54.5 + - - +
487D HIS* 3.8 6.6 - - - +
488D ASP* 2.8 44.3 + - - +
513D TYR* 3.7 9.4 - - - -
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Residues in contact with TRP 485 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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482D ASN* 3.3 27.7 + - + +
483D LEU 3.2 0.2 - - - -
484D GLY* 1.3 73.8 - - - +
486D MET* 1.3 77.5 + - + +
488D ASP* 4.4 3.4 - - - -
489D THR* 2.5 60.5 + - + +
507D LEU 5.9 0.8 + - - -
510D GLY* 4.9 7.4 - - - -
513D TYR* 3.2 10.3 + - - +
521D LEU* 3.7 45.5 - - + -
522D PRO 4.5 0.9 - - - -
523D LEU* 4.2 10.1 - - + -
553D TYR* 3.6 27.6 - + - -
556D TRP* 4.4 7.2 - + - +
557D MET* 3.7 42.0 - - + -
560D PHE* 3.6 38.1 - + + -
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Residues in contact with MET 486 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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482D ASN 3.2 10.6 + - - +
483D LEU* 3.0 22.8 + - + +
485D TRP* 1.3 90.4 - - + +
487D HIS* 1.3 103.7 + - + +
489D THR* 3.4 1.4 + - - -
490D LEU* 3.1 59.3 + - + +
522D PRO* 3.2 28.5 - - + +
523D LEU* 4.2 2.5 - - + -
527D GLU* 3.6 36.8 - - + +
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Residues in contact with HIS 487 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
483D LEU* 2.7 39.1 + - + +
484D GLY* 3.8 6.5 + - - +
486D MET* 1.3 104.2 - - + +
488D ASP* 1.3 58.7 + - - +
490D LEU* 3.8 2.3 - - - +
491D ASP* 2.8 44.4 + - - +
527D GLU* 4.7 5.7 + - - -
532D LYS* 5.5 3.4 + - - -
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Residues in contact with ASP 488 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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484D GLY* 2.8 30.4 + - - +
485D TRP* 3.9 4.1 + - - +
487D HIS* 1.3 73.8 - - - +
489D THR* 1.3 58.7 + - + +
491D ASP* 3.1 10.6 + - - +
492D TYR* 2.8 29.6 + - - +
506D LYS* 3.3 41.3 + - - +
509D PHE* 4.1 22.7 - - - +
510D GLY* 5.7 0.7 + - - -
513D TYR* 4.5 1.9 + - - -
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Residues in contact with THR 489 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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485D TRP* 2.5 61.6 + - + +
486D MET 3.4 1.7 + - - -
488D ASP* 1.3 73.8 - - - +
490D LEU* 1.3 55.3 + - - +
492D TYR* 3.3 8.3 - - - +
493D MET* 2.9 35.1 + - - +
506D LYS 3.9 7.0 - - - +
507D LEU* 3.8 23.8 - - + +
553D TYR* 3.2 28.1 + - + -
556D TRP* 4.3 7.0 - - - +
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Residues in contact with LEU 490 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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486D MET* 3.1 55.2 + - + +
487D HIS* 3.8 3.1 - - - +
489D THR* 1.3 72.9 + - - +
491D ASP* 1.3 69.3 + - - +
493D MET* 3.3 6.4 + - + +
494D LYS* 2.9 30.6 + - - +
523D LEU* 4.2 9.4 - - + -
527D GLU* 5.0 1.8 - - + -
535D ILE* 4.6 15.0 - - + -
538D ARG* 3.7 33.8 - - - +
539D MET* 5.3 1.1 - - + -
553D TYR* 3.1 36.8 - - + +
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Residues in contact with ASP 491 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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487D HIS* 2.8 32.3 + - - +
488D ASP* 3.3 6.6 - - - +
490D LEU* 1.3 77.1 - - - +
492D TYR* 1.3 64.1 + - - +
494D LYS* 3.2 33.2 + - - +
495D LEU* 3.3 16.3 + - - +
506D LYS* 3.9 26.1 + - + -
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Residues in contact with TYR 492 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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488D ASP 2.8 12.4 + - - +
489D THR 3.3 7.6 - - - +
491D ASP* 1.3 77.9 - - - +
493D MET* 1.3 74.7 + - - +
495D LEU* 3.1 27.0 + - + +
500D ARG* 3.1 50.9 + - + +
503D HIS* 3.4 31.9 - - + -
504D HIS* 4.4 6.7 - - - -
506D LYS* 3.8 7.1 - - + +
507D LEU* 3.3 48.5 - - + +
637D SER* 3.6 14.7 + - - -
639D LEU* 4.6 1.7 - - - +
657D PHE* 3.6 30.9 - + - +
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Residues in contact with MET 493 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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489D THR 2.9 22.7 + - - +
490D LEU* 3.3 6.0 + - - +
492D TYR* 1.3 86.6 - - - +
494D LYS* 1.3 60.7 + - - +
500D ARG* 3.1 20.1 + - - +
507D LEU* 5.7 1.3 - - + -
538D ARG 4.1 1.6 - - - +
539D MET* 3.6 34.2 - - + +
540D PRO* 3.2 16.6 - - - +
549D ASN* 3.6 40.4 - - - +
553D TYR* 3.9 30.5 - - + -
657D PHE* 3.7 27.6 - - + -
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Residues in contact with LYS 494 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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490D LEU* 2.9 23.1 + - - +
491D ASP* 3.2 30.3 + - - +
493D MET* 1.3 74.9 - - - +
495D LEU* 1.3 64.8 + - - +
496D ASP 3.6 1.4 + - - -
538D ARG* 3.6 54.6 - - + +
540D PRO* 4.2 8.1 - - - +
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Residues in contact with LEU 495 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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491D ASP 3.5 7.6 - - - +
492D TYR* 3.1 25.9 + - + +
494D LYS* 1.3 79.3 - - - +
496D ASP* 1.3 64.6 + - - +
499D TYR* 4.1 17.9 - - + +
500D ARG* 2.4 40.4 + - - -
503D HIS* 3.3 52.3 - - + +
506D LYS* 4.5 5.2 - - + -
540D PRO* 3.6 2.1 - - - +
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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