Contacts of the strand formed by residues 80 - 87 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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76D ALA* 3.3 5.2 - - - +
77D GLY 2.8 32.5 + - - -
78D ASN 3.0 5.3 + - - +
79D GLY* 1.3 77.9 - - - +
81D VAL* 1.3 63.7 + - - -
97D LYS* 5.0 1.3 - - - -
98D LEU 3.2 12.1 - - - -
99D ILE* 4.4 0.9 - - - -
100D HIS* 4.0 3.9 - - - -
901D ACP 3.5 6.5 + - - -
903D 573 3.3 13.4 + - - -
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Residues in contact with VAL 81 (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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73D GLU* 3.5 25.8 - - - +
75D GLY 3.8 3.6 - - - +
76D ALA* 3.9 10.5 - - + +
80D GLY* 1.3 76.7 - - - +
82D VAL* 1.3 67.6 + - - +
83D PHE* 3.8 28.9 - - + -
96D ARG 3.8 0.7 - - - +
97D LYS* 3.2 4.2 - - - +
98D LEU* 2.8 37.2 + - + +
100D HIS* 3.3 26.2 - - + +
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Residues in contact with VAL 82 (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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73D GLU* 3.7 4.3 - - - +
74D LEU* 2.8 53.4 + - + +
75D GLY 2.9 14.6 + - - +
81D VAL* 1.3 81.1 - - - +
83D PHE* 1.3 59.6 - - - +
95D ALA* 4.2 6.7 - - + -
96D ARG 3.3 13.5 - - - +
97D LYS* 3.9 22.7 - - + -
143D MET* 4.8 0.2 - - + -
901D ACP 3.6 55.2 - - + +
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Residues in contact with PHE 83 (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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70D LYS* 3.9 42.4 - - + -
72D SER 3.6 17.5 - - - +
73D GLU* 3.4 33.9 - - + -
74D LEU* 4.0 4.3 - - - -
81D VAL* 3.8 20.0 - - + -
82D VAL* 1.3 74.1 - - - +
84D LYS* 1.3 60.7 + - - +
85D VAL* 3.6 17.1 + - + -
95D ALA* 3.5 2.1 - - - -
96D ARG* 2.7 44.9 + - + +
98D LEU* 3.5 33.0 - - + -
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Residues in contact with LYS 84 (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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70D LYS* 4.1 0.3 - - - -
71D ILE* 2.9 52.9 + - + +
72D SER* 3.3 28.7 + - - +
74D LEU* 3.6 22.9 - - + +
83D PHE* 1.3 70.0 - - - +
85D VAL* 1.3 64.1 + - - +
93D VAL* 4.0 21.8 - - + -
94D MET 3.4 6.7 - - - +
145D HIS* 3.5 35.0 - - + +
147D ASP* 6.0 0.2 - - - +
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Residues in contact with VAL 85 (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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68D PHE* 3.9 30.5 - - + -
69D GLU 3.2 15.0 - - - +
70D LYS* 4.4 9.2 - - + -
71D ILE* 4.2 5.6 - - - -
83D PHE* 3.9 21.3 - - + +
84D LYS* 1.3 80.3 - - - +
86D SER* 1.3 61.1 + - - +
93D VAL* 3.3 8.0 - - - +
94D MET* 2.9 56.2 + - + +
96D ARG* 4.1 22.2 - - + +
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Residues in contact with SER 86 (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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68D PHE* 3.4 6.1 - - - -
69D GLU* 3.0 45.7 + - - +
71D ILE* 4.3 14.3 - - - +
85D VAL* 1.3 76.2 - - - +
87D HIS* 1.3 69.2 + - - +
88D LYS* 3.2 3.8 + - - -
91D GLY* 4.7 9.1 - - - -
92D LEU 3.3 11.7 - - - -
93D VAL* 4.7 4.9 - - - -
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Residues in contact with HIS 87 (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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67D ASP* 3.5 18.1 - - + +
68D PHE* 4.0 29.8 - + + -
85D VAL* 5.1 0.4 - - - +
86D SER* 1.3 70.1 + - - +
88D LYS* 1.3 60.3 + - - +
89D PRO* 3.5 23.3 - - + +
90D SER* 2.1 41.1 + - - +
91D GLY* 2.7 32.7 + - - -
92D LEU* 3.1 17.8 + - + +
94D MET* 5.3 5.4 - - + +
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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