Contacts of the helix formed by residues 55 - 61 (chain 3) 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 55 (chain 3).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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313 PHE* 4.0 13.7 - - - -
323 PRO* 3.2 36.0 - - - +
343 ILE* 3.4 11.3 + - - +
543 VAL* 1.3 74.9 - - - +
563 ASP* 1.3 65.1 + - - -
583 ALA* 3.2 5.8 + - - +
593 GLN* 3.2 15.9 + - - +
883 HIS* 5.2 1.1 - - - -
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Residues in contact with ASP 56 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303 VAL 4.7 1.9 - - - +
313 PHE* 3.5 19.9 - - - +
323 PRO* 3.7 19.1 - - - +
543 VAL 3.5 1.2 + - - -
553 GLY* 1.3 69.6 - - - -
573 GLU* 1.3 61.1 + - + +
593 GLN* 3.0 5.9 + - + +
603 SER* 2.8 31.9 + - - -
883 HIS* 5.9 0.2 + - - -
933 GLU* 5.0 4.2 - - - +
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Residues in contact with GLU 57 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
473 MET* 6.2 0.2 - - - +
503 LYS* 4.8 6.9 + - - -
533 TYR* 3.4 31.1 + - + -
543 VAL 3.6 9.6 + - - +
553 GLY 3.4 0.6 - - - -
563 ASP* 1.3 76.7 - - - +
583 ALA* 1.3 60.0 + - - +
603 SER* 3.2 15.9 + - - +
613 LYS* 2.8 52.2 + - - +
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Residues in contact with ALA 58 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343 ILE* 4.3 8.3 - - + -
363 GLY* 3.9 14.1 - - - +
533 TYR* 3.8 26.4 - - + +
543 VAL* 4.0 2.7 + - - +
553 GLY 3.2 14.6 + - - +
563 ASP 3.1 0.8 - - - -
573 GLU* 1.3 76.5 - - - +
593 GLN* 1.3 66.7 + - - +
623 ARG* 3.3 13.9 + - - -
653 LEU* 3.7 10.9 - - - +
673 LEU* 3.4 23.3 - - + +
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Residues in contact with GLN 59 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323 PRO* 4.5 9.8 - - + +
343 ILE* 3.7 21.2 - - - +
553 GLY 3.2 10.9 + - - +
563 ASP* 3.0 12.6 + - - +
583 ALA* 1.3 76.8 - - - +
603 SER* 1.3 64.2 + - - +
623 ARG* 3.0 70.4 + - - +
673 LEU* 3.5 21.6 - - - +
693 TYR* 5.0 3.7 + - - -
2073 GLU* 3.8 9.9 - - - +
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Residues in contact with SER 60 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2881 ASP* 4.0 10.2 - - - +
2911 LYS* 4.4 13.9 - - - +
563 ASP* 2.8 14.0 + - - -
573 GLU* 3.2 17.5 + - - +
593 GLN* 1.3 77.0 - - - +
613 LYS* 1.3 75.2 + - - +
623 ARG* 3.6 1.4 + - - +
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Residues in contact with LYS 61 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2881 ASP* 4.3 3.1 - - - -
2911 LYS* 5.3 12.3 - - - +
443 MET* 3.7 37.1 - - + +
533 TYR* 3.7 32.3 - - + -
573 GLU* 2.8 42.6 + - - +
583 ALA 3.8 3.1 - - - -
593 GLN 3.2 0.8 - - - -
603 SER* 1.3 87.0 + - - +
623 ARG* 1.3 61.7 + - - +
633 GLY 3.1 4.3 + - - -
643 ILE* 3.3 23.0 + - + +
653 LEU* 3.4 18.1 - - + +
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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
------------------------------------------------------------
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