Contacts of the strand formed by residues 73 - 78 (chain H) in PDB entry 4EUP
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 ARG 73 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7H SER* 5.2 2.0 - - - -
22H GLU* 2.6 58.8 + - - +
23H CYS 3.3 9.0 - - - +
24H VAL* 3.4 24.5 - - + +
32H MET* 3.9 2.0 - - - -
67H SER 3.8 1.3 - - - +
68H ARG* 3.8 13.3 - - - +
69H GLU* 5.7 1.6 - - + +
70H LYS* 3.0 36.5 + - + +
71H LYS 3.3 2.0 + - - -
72H GLU* 1.3 84.0 - - + +
74H PHE* 1.3 64.5 + - - +
75H SER* 3.9 10.8 - - - +
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Residues in contact with PHE 74 (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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23H CYS* 3.0 24.0 + - + +
32H MET* 3.2 61.2 - - + -
33H PHE 4.0 2.9 - - - -
34H TRP* 2.8 50.0 + + - -
47H TYR* 4.0 11.7 - - + -
48H PHE 4.0 14.1 - - - -
49H SER* 4.0 9.6 - - - -
54H MET 5.3 0.4 - - - -
66H VAL* 3.4 43.3 - - + -
67H SER 3.6 10.1 - - - -
68H ARG* 3.8 17.7 - - + +
73H ARG* 1.3 74.2 - - - +
75H SER* 1.3 57.8 + - - +
91H CYS* 5.8 1.1 - - - -
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Residues in contact with SER 75 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21H LEU 3.7 4.9 - - - -
22H GLU* 2.6 34.4 + - - -
34H TRP* 3.8 0.7 - - - -
66H VAL* 3.0 10.9 - - - +
67H SER* 2.8 53.5 + - - -
73H ARG* 3.9 7.6 - - - +
74H PHE* 1.3 73.0 - - - +
76H LEU* 1.3 61.2 + - - +
77H ILE* 4.1 7.6 - - - -
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Residues in contact with LEU 76 (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 VAL 3.8 0.3 - - - +
20H PHE* 3.8 0.3 - - - -
21H LEU* 2.9 40.9 + - + +
22H GLU* 5.3 0.2 - - - +
34H TRP* 3.4 43.2 - - + +
46H ILE* 4.4 10.3 - - + -
64H TYR* 3.7 34.3 - - + -
65H SER 3.7 5.2 - - - +
66H VAL* 4.2 10.8 - - + -
75H SER* 1.3 73.7 - - - +
77H ILE* 1.3 68.8 + - - +
78H LEU* 4.1 12.1 - - + +
89H TYR* 3.7 33.7 - - + -
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Residues in contact with ILE 77 (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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18H LYS* 4.5 16.2 - - + +
19H VAL 3.4 8.3 - - - +
20H PHE* 3.7 33.4 - - + -
64H TYR* 3.3 6.2 - - - +
65H SER* 2.7 56.7 + - - +
66H VAL 5.3 0.9 - - - -
67H SER* 4.9 17.5 - - - -
75H SER* 5.0 5.8 - - - -
76H LEU* 1.3 80.9 - - - +
78H LEU* 1.3 74.8 + - - +
79H ALA* 3.8 4.9 + - + +
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Residues in contact with LEU 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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17H GLU 4.3 0.5 - - - +
18H LYS* 3.4 5.4 - - - +
19H VAL* 3.0 45.0 + - + +
21H LEU* 3.5 31.6 - - + -
63H GLY 3.7 4.9 - - - -
64H TYR* 3.5 14.4 - - + -
76H LEU* 4.1 14.8 - - + -
77H ILE* 1.3 75.8 - - - +
79H ALA* 1.3 63.7 + - - +
80H SER 3.5 2.0 + - - -
81H ALA* 5.1 4.7 - - + -
85H GLN* 3.8 30.1 - - + +
89H TYR* 3.9 23.8 - - + +
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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