Contacts of the helix formed by residues 77 - 88 (chain K) 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 PHE 77 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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837D MLY 6.4 2.9 - - + -
24K ILE* 3.9 15.7 - - + -
27K PHE* 4.1 2.9 - - + -
28K LYS* 3.5 48.7 - - + -
31K PHE* 3.6 37.3 - + + -
40K GLY 4.0 0.6 + - - -
76K ASN* 1.3 73.6 - - - +
78K THR* 1.3 64.7 + - + +
80K PHE* 3.3 3.9 + + + +
81K LEU* 3.0 64.7 + - + +
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Residues in contact with THR 78 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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837D MLY 6.3 2.9 - - - -
54E MET 5.5 2.9 - - - +
55E GLY* 5.3 13.0 - - - +
76K ASN* 2.8 18.5 + - - +
77K PHE* 1.3 83.8 - - + +
79K VAL* 1.3 63.4 + - - +
81K LEU* 3.7 10.4 - - + +
82K THR* 3.0 38.5 + - - +
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Residues in contact with VAL 79 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71K ALA* 4.1 13.5 - - + -
72K SER 5.5 0.7 - - - +
73K GLY* 4.3 7.4 - - - +
74K PRO* 3.5 26.5 - - + +
75K ILE* 4.0 19.1 - - + -
76K ASN* 3.0 24.3 + - - +
78K THR* 1.3 77.8 - - - +
80K PHE* 1.3 60.6 + - - +
82K THR* 2.9 19.8 + - - +
83K MET* 3.0 18.9 + - + +
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Residues in contact with PHE 80 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
831J TRP* 3.3 44.6 - + - -
27K PHE* 4.6 12.6 - + + -
30K ALA* 4.9 4.5 - - + -
31K PHE* 3.7 39.7 - + + -
34K ILE* 4.4 4.3 - - + -
42K ILE* 4.6 2.9 - - + -
75K ILE* 3.7 20.4 - - + +
76K ASN 3.0 15.7 + - - +
77K PHE* 3.6 7.0 - + + +
79K VAL* 1.3 78.8 - - - +
81K LEU* 1.3 57.8 + - + +
83K MET* 3.4 16.9 + - + +
84K PHE* 3.0 63.2 + + - +
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Residues in contact with LEU 81 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
837D MLY 6.0 5.4 - - - +
19K PHE* 4.5 10.5 - - + -
24K ILE* 4.4 16.8 - - + -
27K PHE* 4.0 31.2 - - + -
77K PHE* 3.0 63.4 + - + +
78K THR* 3.4 11.0 + - + +
80K PHE* 1.3 79.0 - - + +
82K THR* 1.3 59.5 + - + +
84K PHE* 3.4 3.1 + - + +
85K GLY* 2.8 27.2 + - - -
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Residues in contact with THR 82 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78K THR* 3.0 22.0 + - - +
79K VAL* 2.9 20.4 + - - +
81K LEU* 1.3 73.8 - - + +
83K MET* 1.3 59.4 + - - +
85K GLY* 3.7 1.7 - - - +
86K GLU* 3.0 50.2 + - - +
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Residues in contact with MET 83 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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829J TRP* 2.9 34.8 - - + -
831J TRP* 4.5 6.1 - - + +
67K MET 4.6 3.6 - - - +
70K GLU* 3.7 45.1 - - + +
71K ALA* 4.6 3.1 - - + -
75K ILE* 4.9 12.1 - - + -
79K VAL* 3.0 19.3 + - + +
80K PHE* 3.7 26.9 - - + +
82K THR* 1.3 77.9 + - - +
84K PHE* 1.3 60.7 + - - +
86K GLU* 3.3 9.3 + - - +
87K LYS* 3.2 39.0 + - + +
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Residues in contact with PHE 84 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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829J TRP* 2.5 46.4 - + - -
831J TRP* 3.7 18.6 - - + -
832J MET* 3.1 26.0 - - - -
835J PHE* 5.5 3.1 - + + -
19K PHE* 4.3 4.5 - - + -
27K PHE* 4.3 32.3 - + + -
80K PHE* 3.0 55.4 + + - +
81K LEU* 3.9 5.2 - - + +
83K MET* 1.3 78.0 - - - +
85K GLY* 1.3 55.3 + - - +
87K LYS* 3.2 4.6 + - - +
88K LEU* 2.9 54.7 + - + +
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Residues in contact with GLY 85 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19K PHE* 3.5 27.9 - - - -
81K LEU 2.8 15.6 + - - -
82K THR* 3.7 2.5 - - - -
83K MET 3.3 0.2 - - - -
84K PHE* 1.3 75.8 - - - +
86K GLU* 1.3 62.2 + - - +
88K LEU 3.2 15.8 + - - +
89K LYS* 3.2 13.6 - - - +
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Residues in contact with GLU 86 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82K THR* 3.0 33.9 + - - +
83K MET* 3.7 8.7 - - - +
85K GLY* 1.3 75.5 - - - +
87K LYS* 1.3 61.4 + - + +
89K LYS* 3.5 25.4 - - + +
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Residues in contact with LYS 87 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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822J SER* 4.0 10.6 + - - +
825J ASN* 4.4 12.4 + - + +
826J VAL* 3.5 22.8 - - + +
829J TRP* 2.0 85.8 - - + +
70K GLU* 5.6 2.0 - - + +
83K MET* 3.2 25.1 + - + +
84K PHE* 3.2 10.6 + - - +
86K GLU* 1.3 81.6 - - + +
88K LEU* 1.3 60.1 + - + +
89K LYS* 3.5 3.8 + - - -
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Residues in contact with LEU 88 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
822J SER* 3.3 16.4 - - - +
823J PHE* 5.0 0.7 - - - +
826J VAL* 2.8 40.8 - - + -
832J MET* 3.9 19.5 - - + -
19K PHE* 5.2 10.1 - - + -
23K GLU* 5.8 1.3 - - - +
27K PHE* 4.5 12.3 - - + -
84K PHE* 2.9 43.7 + - + +
85K GLY* 3.2 7.4 + - - +
87K LYS* 1.3 78.9 - - + +
89K LYS* 1.3 55.9 + - - +
90K GLY 3.1 10.0 + - - -
91K ALA* 3.2 28.3 + - + +
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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