Contacts of the helix formed by residues 546 - 559 (chain D) in PDB entry 1MVW
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 THR 546 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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544D LYS 4.6 2.9 + - - -
545D ALA* 1.3 78.4 + - - +
547D ASP* 1.3 79.9 + - + +
548D THR* 3.0 27.8 - - - +
549D SER* 2.9 17.0 + - - -
550D PHE* 2.8 23.2 + - - +
596D LEU* 3.5 7.4 - - - +
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Residues in contact with ASP 547 (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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546D THR* 1.3 77.7 - - + +
548D THR* 1.3 52.5 + - - +
550D PHE* 3.0 12.1 - - - +
551D MLY 2.7 36.6 + - - +
592D ILE* 3.7 18.3 - - - +
593D SER* 3.3 9.3 - - - -
594D GLY* 2.9 29.6 + - - -
595D TRP* 4.5 0.6 - - - +
596D LEU* 3.4 32.4 + - - +
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Residues in contact with THR 548 (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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546D THR* 3.0 16.8 - - + +
547D ASP* 1.3 80.3 - - - +
549D SER* 1.3 62.6 + - - +
551D MLY 3.3 28.4 + - - +
552D ASN* 2.8 35.4 + - - +
47W MET* 2.9 6.8 - - - +
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Residues in contact with SER 549 (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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539D GLU* 2.8 24.2 + - - +
544D LYS 5.6 0.2 - - - -
545D ALA* 4.2 1.8 - - - -
546D THR* 2.9 31.7 + - - -
548D THR* 1.3 84.7 - - - +
550D PHE* 1.3 66.7 + - - +
552D ASN 3.0 0.9 + - - -
45W VAL* 2.4 23.9 - - - +
46W GLY* 2.2 31.5 - - - +
47W MET* 2.6 7.9 + - - +
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Residues in contact with PHE 550 (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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532D ILE* 4.9 3.4 - - + -
535D ILE* 3.9 21.3 - - + -
536D LEU* 3.2 53.8 - - + -
539D GLU* 4.1 3.8 - - + -
546D THR 2.8 10.0 + - - +
547D ASP* 3.0 7.9 - - - +
549D SER* 1.3 73.1 + - - +
551D MLY 1.3 52.5 + - - +
553D MLY 3.5 0.2 - - - +
554D LEU* 2.9 29.3 + - + +
592D ILE* 3.0 41.5 - - + -
595D TRP* 4.1 16.6 - + + -
596D LEU* 3.8 17.7 - - + -
46W GLY* 1.1 63.8 - - - +
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Residues in contact with MLY 551 (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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547D ASP 2.7 19.6 + - - +
548D THR* 3.5 31.1 + - - +
549D SER 3.1 0.4 + - - -
550D PHE* 1.3 72.1 + - - +
552D ASN* 1.3 68.9 + - - +
554D LEU* 2.7 27.5 + - + +
555D TYR* 3.0 41.3 + - + +
576D GLU* 5.3 4.5 - - - -
577D ALA* 5.0 2.5 - - - -
578D HIS* 3.8 34.8 - - + +
592D ILE* 4.4 17.5 - - + -
46W GLY 2.5 10.2 - - - +
47W MET* 2.7 0.2 - - - +
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Residues in contact with ASN 552 (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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548D THR* 2.8 25.7 + - - +
549D SER* 4.3 0.2 - - - +
551D MLY 1.3 82.6 + - - -
553D MLY 1.3 7.0 - - - -
555D TYR* 2.9 4.7 + - - -
556D ASP 2.9 1.2 + - - -
44W MET* 4.6 1.8 - - + -
46W GLY 2.7 1.6 + - - -
47W MET* 0.8 425.7 - - + +
48W GLY 1.2 52.6 + - - -
50W LYS* 5.9 3.8 - - - +
53W TYR* 6.0 1.6 - - - +
57W GLU* 5.2 9.8 + - - +
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Residues in contact with MLY 553 (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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1679 GLU 5.2 3.1 - - - -
3559 MET* 5.5 1.3 - - - -
535D ILE* 3.9 16.9 - - + +
538D GLU* 4.3 17.5 - - - +
539D GLU* 3.0 12.8 + - - +
542D PHE* 3.3 32.8 - - - -
550D PHE 3.5 0.4 - - - +
552D ASN 1.3 6.1 - - - -
554D LEU* 1.3 53.2 + - - +
557D GLU* 3.6 11.4 + - - +
43W VAL* 4.2 16.6 - - + -
44W MET 2.2 27.1 - - - +
45W VAL* 1.1 84.8 - - - +
46W GLY* 1.6 58.1 + - - +
47W MET* 0.9 148.9 + - - +
48W GLY* 2.5 12.8 + - - -
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Residues in contact with LEU 554 (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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532D ILE* 4.1 23.3 - - + -
535D ILE* 3.4 35.7 - - + -
550D PHE* 2.9 32.6 + - + +
551D MLY 2.8 15.0 - - + +
553D MLY 1.3 75.8 + - - +
555D TYR* 1.3 60.9 + - + +
558D HIS* 3.1 31.2 + - + +
565D PHE* 4.1 17.4 - - + -
579D PHE* 3.9 31.4 - - + -
592D ILE* 4.4 5.8 - - + -
46W GLY 2.5 7.7 + - - -
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Residues in contact with TYR 555 (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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551D MLY 3.0 54.9 + - + +
552D ASN* 2.9 3.9 + - - +
554D LEU* 1.3 70.1 - - + +
556D ASP* 1.3 56.6 + - - +
557D GLU 2.7 12.9 + - - -
558D HIS 2.7 0.3 + - - -
559D LEU* 2.7 61.4 + - + +
565D PHE* 3.8 17.5 - + - -
567D LYS* 4.4 12.9 - - + +
568D PRO* 4.5 4.7 - - - +
578D HIS* 2.9 30.9 + - - -
579D PHE* 4.9 0.4 - - + -
47W MET* 4.2 8.5 - - + -
48W GLY* 2.3 16.4 - - - +
49W GLN 3.4 3.2 - - - +
50W LYS* 5.3 7.2 - - + -
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Residues in contact with ASP 556 (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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552D ASN 3.6 4.4 - - - +
555D TYR* 1.3 66.7 - - - +
557D GLU* 1.3 46.5 + - - -
559D LEU 5.0 1.2 - - - +
42W GLY 4.4 1.7 - - - +
43W VAL* 3.5 13.3 - - + -
44W MET* 3.6 19.9 + - - +
47W MET* 3.5 11.2 - - - +
48W GLY* 0.9 203.0 + - - +
49W GLN* 1.0 139.9 - - - +
50W LYS* 2.7 35.9 + - - +
53W TYR* 4.1 9.1 + - - -
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Residues in contact with GLU 557 (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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530D MET* 3.6 40.1 - - - +
535D ILE* 4.2 5.8 - - + -
553D MLY 3.6 14.8 - - - +
554D LEU 4.2 0.9 - - - +
555D TYR 2.7 0.6 + - - -
556D ASP 1.3 70.6 - - - -
558D HIS* 1.3 82.6 + - + +
559D LEU 5.2 0.2 - - - -
561D LYS* 4.2 32.4 + - - +
43W VAL* 4.9 8.8 - - + +
47W MET 4.9 0.7 - - - +
48W GLY* 2.1 20.2 - - - -
49W GLN* 2.0 8.7 - - - +
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Residues in contact with HIS 558 (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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525D LEU* 3.7 26.4 - - + +
530D MET* 2.7 31.1 + - + -
531D GLY* 3.6 16.1 - - - -
532D ILE* 4.1 6.7 + - + -
535D ILE* 3.8 9.1 - - + +
554D LEU* 3.1 26.9 + - + +
555D TYR 2.7 4.9 + - - -
557D GLU* 1.3 91.8 + - + +
559D LEU* 1.3 64.5 + - - +
560D GLY 3.3 0.2 + - - -
561D LYS* 3.1 2.1 + - - -
562D SER* 2.8 39.4 + - - +
565D PHE* 3.7 25.0 - + + -
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Residues in contact with LEU 559 (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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555D TYR* 2.7 54.4 + - + +
556D ASP 5.0 1.4 - - - +
557D GLU 5.2 0.2 - - - -
558D HIS* 1.3 73.5 + - - +
560D GLY* 1.3 67.8 - - - +
561D LYS* 3.0 8.2 + - - +
565D PHE* 3.6 20.4 - - + +
566D GLN* 5.1 0.9 - - - -
567D LYS* 4.2 33.0 - - + +
49W GLN* 4.3 10.4 - - - +
51W ASP* 5.7 4.9 - - - +
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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