Contacts of the strand formed by residues 80 - 87 (chain H) in PDB entry 4MNE
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 80 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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76H ALA* 3.6 0.9 - - - +
77H GLY 3.0 28.7 + - - +
78H ASN 3.6 1.4 - - - -
79H GLY* 1.3 79.8 - - - +
81H VAL* 1.3 66.7 + - - +
97H LYS* 5.3 1.3 - - - -
98H LEU 3.3 11.0 - - - -
99H ILE* 4.4 2.7 - - - -
100H HIS* 5.3 0.7 - - - -
901H ACP 3.4 12.9 + - - -
903H 573 3.5 13.0 + - - +
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Residues in contact with VAL 81 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73H GLU* 3.5 25.6 - - - +
75H GLY 3.8 6.5 - - - +
76H ALA* 4.3 7.4 - - + +
80H GLY* 1.3 78.8 - - - +
82H VAL* 1.3 67.8 + - - +
83H PHE* 3.4 30.5 - - + -
96H ARG 3.8 0.3 - - - +
97H LYS* 3.3 3.7 - - - +
98H LEU* 2.8 39.8 + - + +
100H HIS* 6.3 1.3 - - - +
138H GLU* 5.9 2.2 - - - +
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Residues in contact with VAL 82 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73H GLU* 3.8 5.5 - - - +
74H LEU* 2.8 47.7 + - + -
75H GLY 2.9 15.1 + - - +
81H VAL* 1.3 80.6 - - - +
83H PHE* 1.3 67.2 + - - +
95H ALA* 4.3 4.7 - - + -
96H ARG 3.3 11.7 - - - +
97H LYS* 3.5 35.4 - - + -
143H MET* 5.5 0.7 - - + -
901H ACP 3.8 44.2 - - + +
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Residues in contact with PHE 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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70H LYS* 4.0 29.8 - - + -
72H SER 3.4 17.0 - - - +
73H GLU* 4.0 24.5 - - + -
74H LEU* 3.9 4.7 - - - +
81H VAL* 3.4 27.8 - - + -
82H VAL* 1.3 75.0 - - - +
84H LYS* 1.3 61.2 + - - +
85H VAL* 3.6 19.1 + - + -
95H ALA* 3.3 4.0 - - - -
96H ARG* 2.7 42.3 + - + +
98H LEU* 3.5 31.2 - - + -
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Residues in contact with LYS 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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70H LYS* 3.7 0.3 - - - -
71H ILE* 2.6 55.0 + - + -
72H SER* 3.0 24.0 + - - +
74H LEU* 3.4 26.2 - - + +
83H PHE* 1.3 70.8 - - - +
85H VAL* 1.3 58.8 + - - +
93H VAL* 3.6 24.4 - - + +
94H MET 3.6 9.9 - - - +
145H HIS* 3.3 34.7 + - + +
147H ASP* 5.6 1.6 - - - +
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Residues in contact with VAL 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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68H PHE* 3.6 35.2 - - + -
69H GLU 3.4 10.3 - - - +
70H LYS* 3.9 16.8 - - + +
71H ILE* 4.0 5.4 - - - -
83H PHE* 3.6 21.1 + - + +
84H LYS* 1.3 79.7 - - - +
86H SER* 1.3 59.5 + - - +
93H VAL* 3.6 1.4 - - - +
94H MET* 2.8 49.2 + - + +
96H ARG* 3.9 23.1 - - + +
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Residues in contact with SER 86 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68H PHE* 3.6 6.4 - - - -
69H GLU* 3.2 47.4 + - - +
71H ILE* 3.8 16.7 - - - +
85H VAL* 1.3 74.5 - - - +
87H HIS* 1.3 67.7 + - - +
88H LYS* 3.6 2.6 + - - +
91H GLY* 4.4 6.7 - - - -
92H LEU 3.3 8.1 - - - -
93H VAL* 4.1 12.8 - - - +
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Residues in contact with HIS 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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67H ASP* 3.6 36.1 + - + +
68H PHE* 4.3 16.0 - + + -
86H SER* 1.3 73.5 + - - +
88H LYS* 1.3 58.9 + - - +
89H PRO* 3.3 24.5 - - + -
90H SER* 3.2 37.7 + - - +
91H GLY* 2.8 31.9 + - - -
92H LEU 2.8 14.6 + - - +
94H MET* 4.9 0.6 - - - -
904H 573 3.5 34.2 - - + +
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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
------------------------------------------------------------
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