Contacts of the helix formed by residues 90 - 101 (chain E) in PDB entry 5UHA
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 LYS 90 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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459D ARG* 6.0 2.8 - - - +
489D GLU 3.6 10.1 + - - -
490D VAL* 3.6 21.9 + - - +
492D ALA* 3.2 44.9 - - + +
493D GLU* 4.7 9.4 - - + +
494D HIS* 5.4 7.9 - - + +
552D GLN* 5.8 3.6 - - - +
88E GLN* 4.4 7.9 + - - +
89E GLU* 1.3 77.9 - - - +
91E PRO* 1.3 78.7 - - + +
92E LEU* 4.4 6.7 - - + +
93E SER* 3.0 22.6 + - - +
94E ILE* 3.1 13.7 + - - +
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Residues in contact with PRO 91 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61E ALA* 3.8 26.9 - - + +
64E ILE* 3.8 14.4 - - + +
65E ASN* 4.8 16.2 - - + +
89E GLU 3.8 4.2 - - - +
90E LYS* 1.3 90.9 - - + +
92E LEU* 1.3 64.7 + - + +
94E ILE* 3.1 16.7 + - + +
95E ALA* 2.9 22.9 + - - +
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Residues in contact with LEU 92 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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549D ALA 4.2 6.3 - - - +
552D GLN* 4.0 22.9 - - + +
553D ALA* 3.7 40.8 - - + +
556D ARG* 3.6 32.1 - - + +
557D ILE* 6.5 0.2 - - + -
57E ALA* 5.3 4.7 - - + -
58E ALA* 5.7 1.3 - - - -
61E ALA* 3.9 17.0 - - + +
90E LYS* 3.2 5.0 - - + +
91E PRO* 1.3 81.6 - - + +
93E SER* 1.3 54.8 + - - +
95E ALA* 3.3 2.3 + - - +
96E LEU* 2.7 57.7 + - + +
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Residues in contact with SER 93 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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493D GLU* 3.4 24.7 + - - -
556D ARG* 4.4 11.5 + - - +
37E ASN 5.3 3.3 + - - -
38E PRO* 5.4 1.3 - - - +
89E GLU* 3.0 22.5 + - - +
90E LYS* 3.0 19.6 + - - +
92E LEU* 1.3 78.8 - - - +
94E ILE* 1.3 57.4 + - - +
96E LEU* 4.0 4.4 - - - +
97E ARG* 3.1 34.8 + - - +
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Residues in contact with ILE 94 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64E ILE* 3.8 26.0 - - + -
68E TYR* 4.9 11.0 - - + +
81E PRO* 3.9 22.0 - - + -
83E VAL* 4.6 14.9 - - + +
85E PRO* 4.7 15.5 - - + -
89E GLU* 3.4 36.3 - - + +
90E LYS 3.2 15.3 - - - +
91E PRO* 3.1 14.3 + - + +
93E SER* 1.3 74.7 - - - +
95E ALA* 1.3 66.6 + - - +
97E ARG* 3.1 6.2 + - - +
98E GLU* 3.0 27.7 + - - +
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Residues in contact with ALA 95 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57E ALA* 3.9 19.5 - - + +
60E ARG* 3.6 24.5 - - + -
61E ALA* 4.0 8.5 - - + +
64E ILE* 3.9 2.4 - - + +
91E PRO 2.9 12.9 + - - +
92E LEU* 3.6 6.1 - - - +
94E ILE* 1.3 76.4 - - - +
96E LEU* 1.3 62.4 + - - +
98E GLU* 3.1 16.6 - - - +
99E ILE* 3.0 29.1 + - - +
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Residues in contact with LEU 96 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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553D ALA* 6.5 0.2 - - + -
556D ARG* 3.6 45.5 - - - +
557D ILE* 4.8 15.7 - - + -
38E PRO* 3.6 23.9 - - + +
43E LEU* 3.8 23.0 - - + +
53E LEU* 5.1 3.8 - - + -
57E ALA* 3.6 28.7 - - + -
92E LEU* 2.7 28.0 + - + +
93E SER* 4.0 5.4 - - - +
95E ALA* 1.3 73.2 - - - +
97E ARG* 1.3 63.4 + - - +
99E ILE* 3.5 13.4 - - + +
100E HIS 3.5 11.6 + - - -
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Residues in contact with ARG 97 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37E ASN* 4.6 15.7 - - - +
38E PRO* 4.0 19.1 - - + -
83E VAL* 3.6 21.0 - - + +
84E GLU* 2.8 42.0 + - - +
86E GLY* 4.7 3.0 - - - +
89E GLU* 2.9 30.4 + - - +
93E SER* 3.1 26.8 + - - +
94E ILE 3.1 6.0 + - - +
96E LEU* 1.3 78.3 - - - +
98E GLU* 1.3 58.1 + - - +
100E HIS* 3.0 23.7 + - - +
101E ALA* 3.4 6.4 + - - +
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Residues in contact with GLU 98 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60E ARG* 2.4 45.1 + - - +
64E ILE* 4.0 2.9 - - - +
81E PRO 4.2 0.2 - - - -
82E LEU* 3.2 34.0 + - - +
83E VAL* 4.3 18.0 + - + +
94E ILE* 3.0 17.6 + - - +
95E ALA* 3.1 18.1 - - - +
97E ARG* 1.3 73.9 - - - +
99E ILE* 1.3 64.3 + - - +
101E ALA* 3.3 12.9 + - - +
103E LEU* 3.2 32.6 + - + +
104E LEU* 3.8 15.2 + - + -
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Residues in contact with ILE 99 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43E LEU* 3.9 15.3 - - + -
46E ARG* 3.5 17.5 - - + +
53E LEU* 4.2 11.0 - - + -
56E TYR* 3.4 47.6 + - + +
57E ALA* 3.7 28.9 - - + -
95E ALA 3.0 25.3 + - - +
96E LEU* 3.5 19.5 - - + +
98E GLU* 1.3 79.0 - - - +
100E HIS* 1.3 57.5 + - - +
102E ASP* 3.0 23.7 + - - +
104E LEU* 4.2 11.7 - - + -
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Residues in contact with HIS 100 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38E PRO* 3.9 25.8 - - + -
39E PRO* 4.8 2.1 - - + +
42E GLU* 2.4 45.1 + - + +
43E LEU* 4.1 11.9 - - + +
46E ARG* 3.3 26.3 + - - +
96E LEU 3.5 7.2 + - - +
97E ARG 3.0 13.9 + - - +
99E ILE* 1.3 78.4 - - - +
101E ALA* 1.3 56.4 + - - +
102E ASP* 3.1 12.2 - - - +
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Residues in contact with ALA 101 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83E VAL* 4.9 5.6 - - + -
97E ARG 3.4 7.5 + - - +
98E GLU* 3.3 7.3 + - - +
99E ILE 3.1 1.0 - - - -
100E HIS* 1.3 77.8 + - - +
102E ASP* 1.3 67.5 + - - +
103E LEU* 3.0 37.6 + - + +
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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