Contacts of the helix formed by residues 77 - 88 (chain H) 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 H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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24H ILE* 3.9 16.2 - - + -
27H PHE 4.1 2.5 - - - -
28H LYS* 3.5 48.2 - - + -
31H PHE* 3.6 36.2 - + + -
40H GLY 4.0 0.6 + - - -
76H ASN* 1.3 74.6 - - - +
78H THR* 1.3 66.0 + - + +
80H PHE* 3.3 4.5 + + + +
81H LEU* 3.0 65.0 + - + +
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Residues in contact with THR 78 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76H ASN* 2.8 18.4 + - - +
77H PHE* 1.3 84.5 - - + +
79H VAL* 1.3 63.3 + - - +
81H LEU* 3.7 9.5 - - + +
82H THR* 3.0 38.9 + - - +
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Residues in contact with VAL 79 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71H ALA* 4.1 13.9 - - + -
72H SER 5.5 0.9 - - - +
73H GLY* 4.3 7.6 - - - +
74H PRO* 3.5 25.6 - - + +
75H ILE* 4.0 19.5 - - + -
76H ASN* 3.0 24.5 + - - +
78H THR* 1.3 77.2 - - - +
80H PHE* 1.3 60.5 + - - +
82H THR* 2.9 20.4 + - - +
83H MET* 3.0 18.3 + - + +
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Residues in contact with PHE 80 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
831G TRP* 3.7 36.3 - + + -
27H PHE* 4.6 13.5 - + + -
30H ALA* 4.9 4.3 - - + -
31H PHE* 3.7 40.6 - + + -
34H ILE* 4.4 6.7 - - + -
42H ILE* 4.6 2.5 - - + -
75H ILE* 3.7 22.0 - - + -
76H ASN 3.0 15.8 + - - +
77H PHE* 3.6 7.4 - + + +
79H VAL* 1.3 77.2 - - - +
81H LEU* 1.3 57.7 + - + +
83H MET* 3.4 20.5 + - + +
84H PHE* 3.0 65.9 + + - +
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Residues in contact with LEU 81 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19H PHE* 4.5 10.8 - - + -
24H ILE* 4.4 17.5 - - + -
27H PHE* 4.0 30.5 - - + -
77H PHE* 3.0 63.3 + - + +
78H THR* 3.7 10.3 - - + +
80H PHE* 1.3 80.9 - - + +
82H THR* 1.3 58.0 + - + +
84H PHE* 3.4 4.1 + - + +
85H GLY* 2.8 26.7 + - - -
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Residues in contact with THR 82 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78H THR* 3.0 21.1 + - - +
79H VAL* 2.9 21.1 + - - +
81H LEU* 1.3 74.0 - - + +
83H MET* 1.3 59.6 + - - +
85H GLY* 3.3 1.9 + - - +
86H GLU* 3.0 49.5 + - - +
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Residues in contact with MET 83 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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829G TRP* 3.0 35.4 - - + -
831G TRP* 4.9 4.7 - - + +
67H MET 4.6 4.5 - - - +
70H GLU* 3.7 43.3 - - + +
71H ALA* 4.6 2.5 - - + -
75H ILE* 4.9 12.8 - - + -
79H VAL* 3.0 19.3 + - + +
80H PHE* 3.8 26.5 - - + +
82H THR* 1.3 80.0 + - - +
84H PHE* 1.3 62.2 + - + +
86H GLU* 3.3 9.2 + - - +
87H LYS* 3.2 37.8 + - + +
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Residues in contact with PHE 84 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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829G TRP* 2.8 40.4 - + - -
831G TRP* 4.2 14.4 - - + -
832G MET* 2.7 33.2 - - + -
835G PHE* 5.2 3.8 - + + -
19H PHE* 4.3 4.3 - - + -
27H PHE* 4.3 30.3 - + + -
80H PHE* 3.0 56.0 + + - +
81H LEU* 3.9 4.7 - - + +
83H MET* 1.3 77.8 - - - +
85H GLY* 1.3 54.8 + - - +
87H LYS* 3.2 8.4 + - - +
88H LEU* 2.9 55.4 + - + +
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Residues in contact with GLY 85 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19H PHE* 3.5 27.9 - - - -
81H LEU 2.8 15.4 + - - -
82H THR* 3.7 2.5 - - - -
83H MET 3.3 0.4 - - - -
84H PHE* 1.3 74.7 - - - +
86H GLU* 1.3 61.6 + - - +
88H LEU* 3.2 16.3 + - - -
89H LYS* 3.2 14.3 - - - +
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Residues in contact with GLU 86 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82H THR* 3.0 34.2 + - - +
83H MET* 3.7 8.0 - - - +
85H GLY* 1.3 76.1 - - - +
87H LYS* 1.3 62.2 + - + +
89H LYS* 3.5 23.9 - - + +
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Residues in contact with LYS 87 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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822G SER* 3.7 12.5 + - - +
825G ASN* 5.0 6.0 + - + +
826G VAL* 4.1 19.0 - - + +
829G TRP* 2.3 71.7 - - + +
70H GLU* 5.5 3.1 - - + +
83H MET* 3.2 26.9 + - + +
84H PHE* 3.2 16.1 + - - +
86H GLU* 1.3 80.0 - - + +
88H LEU* 1.3 64.0 + - - +
89H LYS* 3.5 4.3 + - - -
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Residues in contact with LEU 88 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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822G SER* 3.2 20.0 - - - +
823G PHE* 4.8 0.7 - - - +
826G VAL* 3.2 35.4 - - + -
832G MET* 4.2 17.0 - - + -
19H PHE* 5.2 10.2 - - + -
23H GLU* 5.8 1.3 - - - +
27H PHE* 4.5 11.0 - - + -
84H PHE* 2.9 45.9 + - + +
85H GLY* 3.2 7.7 + - - +
87H LYS* 1.3 77.3 - - + +
89H LYS* 1.3 56.1 + - - +
90H GLY 3.1 9.5 + - - -
91H ALA* 3.2 27.5 + - + +
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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