Contacts of the helix formed by residues 594 - 601 (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 GLY 594 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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547D ASP* 2.9 13.4 + - - -
593D SER* 1.3 74.7 - - - +
595D TRP* 1.3 60.0 + - - +
596D LEU 3.2 2.7 - - - -
597D GLU* 3.1 12.9 + - - +
598D MLY 2.7 48.2 + - - +
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Residues in contact with TRP 595 (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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473D ASN 4.5 1.8 - - - -
474D SER* 2.8 20.0 + - - -
475D PHE* 3.0 40.5 - + + +
478D LEU* 4.0 28.0 - - + -
532D ILE* 5.3 1.3 - - + -
536D LEU* 3.9 26.7 - - + -
547D ASP* 4.0 0.8 + - - +
550D PHE* 4.1 21.8 - + + -
579D PHE* 4.4 16.4 - + - -
590D TYR* 4.3 15.9 - - + -
591D ASN 2.8 32.0 + - - -
592D ILE* 3.5 9.6 - - + -
593D SER 3.1 17.2 - - - +
594D GLY* 1.3 81.1 - - - +
596D LEU* 1.3 56.2 + - - +
598D MLY 3.6 7.9 - - - +
599D ASN* 2.6 40.2 + - - +
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Residues in contact with LEU 596 (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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536D LEU* 3.8 18.8 - - + -
539D GLU* 4.6 11.2 - - + +
540D CYS* 3.8 13.6 - - - -
545D ALA* 3.8 27.8 - - + +
546D THR* 3.5 31.0 - - - +
547D ASP* 3.4 12.6 + - - +
550D PHE* 3.8 27.6 - - + -
594D GLY 3.2 0.4 - - - -
595D TRP* 1.3 79.3 - - - +
597D GLU* 1.3 63.4 + - + +
599D ASN* 3.4 3.5 + - - +
600D MLY 3.2 40.9 + - - +
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Residues in contact with GLU 597 (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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594D GLY* 3.1 13.8 + - - +
596D LEU* 1.3 76.2 - - - +
598D MLY 1.3 60.1 + - - +
599D ASN 2.9 1.6 - - - -
600D MLY 2.5 33.1 + - - -
601D ASP 3.2 9.7 + - - -
602D PRO* 3.3 31.1 - - + +
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Residues in contact with MLY 598 (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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272D MLY 4.8 10.1 - - - -
431D MLY 6.4 2.0 - - - -
472D PHE* 5.8 3.4 - - - -
474D SER* 4.2 16.4 + - - -
475D PHE* 3.9 22.5 - - + +
476D GLU* 2.7 40.6 + - + +
593D SER 3.6 23.8 - - - -
594D GLY* 2.7 30.5 + - - +
595D TRP* 3.6 6.7 - - - +
597D GLU* 1.3 74.1 + - - +
599D ASN* 1.3 62.0 + - - +
600D MLY 3.4 0.2 + - - -
601D ASP* 3.7 6.3 + - - +
602D PRO* 5.5 0.7 - - - -
649D VAL* 3.2 17.9 - - - +
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Residues in contact with ASN 599 (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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475D PHE* 3.6 8.3 - - + -
536D LEU* 3.6 26.0 + - + +
537D GLU* 4.4 1.0 - - - +
540D CYS* 4.0 11.4 - - - -
595D TRP 2.6 20.2 + - - +
596D LEU 3.6 4.9 - - - +
598D MLY 1.3 77.6 + - - +
600D MLY 1.3 59.8 + - - +
601D ASP 3.5 0.2 - - - -
647D GLN 4.6 0.5 - - - +
648D THR* 2.8 18.1 + - - +
649D VAL* 2.0 83.3 + - + +
650D SER* 2.7 24.2 + - - -
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Residues in contact with MLY 600 (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 3.8 3.6 - - - -
540D CYS* 3.3 45.8 - - + +
541D MET 4.6 0.2 - - - -
542D PHE 2.8 33.7 - - - -
543D PRO* 4.1 13.9 - - - -
545D ALA* 4.7 14.4 - - - -
596D LEU* 3.2 28.5 - - - +
597D GLU* 2.5 23.5 + - - +
599D ASN* 1.3 74.5 + - - +
601D ASP* 1.3 69.1 + - - +
602D PRO* 3.9 11.0 - - + -
640D LYS* 3.2 29.9 + - - +
646D PHE 5.3 1.6 - - - +
647D GLN 5.4 4.0 - - - +
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Residues in contact with ASP 601 (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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272D MLY 3.5 39.6 + - - -
428D ALA* 6.0 0.3 - - - +
432D ALA* 5.5 0.5 - - - +
436D MLY 3.6 19.9 - - - -
597D GLU 3.2 2.0 + - - -
598D MLY 3.7 3.4 + - - +
599D ASN 3.5 1.4 - - - -
600D MLY 1.3 80.3 + - - +
602D PRO* 1.3 72.2 - - - +
603D LEU* 3.4 23.4 + - - +
640D LYS* 5.0 1.6 + - - -
646D PHE* 6.6 0.2 - - + -
649D VAL* 4.0 16.2 - - + -
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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