Contacts of the strand formed by residues 71 - 80 (chain N) in PDB entry 4EMG
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 ILE 71 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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52N GLU* 3.8 0.9 - - - +
53N ILE* 3.8 0.7 - - - -
54N VAL* 2.8 54.5 + - + +
70N THR* 1.3 77.9 - - - +
72N ARG* 1.3 68.6 + - - +
73N LYS* 5.5 4.4 - - + +
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Residues in contact with ARG 72 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51N GLU* 2.7 30.5 + - + +
52N GLU 3.3 5.2 - - - +
53N ILE* 3.4 32.7 - - + +
70N THR* 2.8 45.9 + - + +
71N ILE* 1.3 82.9 - - - +
73N LYS* 1.3 66.7 + - - +
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Residues in contact with LYS 73 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23H TYR* 4.0 27.4 - - - +
31H GLU* 4.6 5.8 - - - +
51N GLU* 3.4 7.3 - - - +
52N GLU* 2.8 47.5 + - - +
71N ILE* 5.9 4.3 - - + -
72N ARG* 1.3 77.7 - - - +
74N HIS* 1.3 65.7 + - - +
75N TYR* 3.1 41.6 + - + +
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Residues in contact with HIS 74 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92H ARG* 2.4 47.9 + - - +
49N ASP* 3.6 36.5 + - - -
50N ALA 3.3 20.2 - - - -
51N GLU* 4.7 6.7 - - + -
73N LYS* 1.3 79.5 + - - +
75N TYR* 1.3 81.2 + - - +
76N GLU* 4.2 1.6 - - - -
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Residues in contact with TYR 75 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23H TYR* 3.3 22.1 + + + -
87H LEU* 4.4 1.6 - - + +
89H ALA* 3.4 30.1 - - + -
92H ARG* 4.2 1.8 - - - +
49N ASP* 3.3 2.9 - - - -
50N ALA* 2.7 46.6 + - + +
52N GLU* 2.7 41.3 + - + -
73N LYS* 3.1 41.8 + - + +
74N HIS* 1.3 84.3 - - - +
76N GLU* 1.3 61.7 + - - +
77N MSE 3.8 14.6 - - - +
78N LEU* 3.8 32.3 - - + -
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Residues in contact with GLU 76 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92H ARG* 3.5 57.2 - - + +
93H ASN* 4.1 18.0 + - - -
48N GLY* 3.4 4.0 - - - -
49N ASP* 2.7 29.8 + - - +
74N HIS* 4.5 2.9 - - - -
75N TYR* 1.3 70.4 - - - +
77N MSE 1.3 69.5 + - + +
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Residues in contact with MSE 77 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13H LEU* 4.1 17.5 - - + -
89H ALA* 3.9 3.5 - - - +
90H PRO* 3.1 37.8 - - + +
37N HIS* 3.6 33.4 - - + +
46N VAL* 3.9 21.1 - - + -
47N LEU 3.5 1.3 - - - -
48N GLY* 3.9 5.2 - - - -
75N TYR* 3.8 9.8 - - - +
76N GLU* 1.3 98.0 - - + +
78N LEU* 1.3 61.5 + - - +
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Residues in contact with LEU 78 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13H LEU* 3.8 4.6 - - - +
23H TYR* 5.6 0.2 - - + -
87H LEU* 4.2 21.1 - - + -
88H ILE 4.0 8.5 - - - +
89H ALA* 4.1 4.5 - - + -
32N LEU* 3.9 37.5 - - + -
45N MSE 3.6 0.5 - - - +
46N VAL* 3.1 4.4 - - - +
47N LEU* 2.7 45.2 + - + +
50N ALA* 4.1 13.9 - - + -
75N TYR* 3.8 48.2 - - + -
77N MSE 1.3 75.1 - - - +
79N PHE* 1.3 67.7 + - - +
80N VAL* 3.8 5.7 + - + -
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Residues in contact with PHE 79 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10H PRO* 3.5 23.6 - - + -
11H LEU* 3.7 24.0 - - + -
13H LEU* 3.5 15.9 - - + +
14H VAL* 4.2 9.9 - - + -
43H LEU* 3.7 31.4 - - + -
85H VAL* 5.4 1.1 - - + -
86H ILE 4.9 0.9 - - - -
87H LEU* 3.3 9.5 - - - +
88H ILE* 2.8 61.0 + - + +
44N ASN* 3.9 32.1 - - + -
45N MSE 3.4 10.1 - - - -
46N VAL* 4.3 1.1 - - + -
78N LEU* 1.3 72.7 - - - +
80N VAL* 1.3 69.5 + - - +
81N ARG* 3.8 7.6 - - + -
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Residues in contact with VAL 80 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86H ILE 3.8 2.2 - - - +
87H LEU* 4.1 10.5 - - + -
26N LEU* 3.9 28.7 - - + -
32N LEU* 3.5 27.6 - - + -
44N ASN* 3.3 5.7 - - - +
45N MSE 2.7 49.1 + - + +
47N LEU* 4.1 15.3 - - + -
78N LEU* 4.2 9.6 - - + +
79N PHE* 1.3 79.5 - - - +
81N ARG* 1.3 72.1 + - - +
84N SER* 4.7 0.2 - - - +
85N VAL* 4.3 8.1 - - + -
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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