Contacts of the helix formed by residues 105 - 115 (chain E) in PDB entry 5HMG
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 TYR 105 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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65E THR* 3.2 29.7 - - + +
67E ILE* 3.6 35.0 - - + +
100E TYR* 4.3 11.3 + + - -
102E VAL* 3.0 41.7 + - + +
104E ASP* 1.3 76.0 - - - +
106E ALA* 1.3 65.1 + - - +
108E LEU* 3.2 2.1 + - - +
109E ARG* 2.9 40.3 + - + +
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Residues in contact with ALA 106 (chain E).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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76D ARG* 3.9 36.6 - - + +
104E ASP* 3.7 10.1 - - - +
105E TYR* 1.3 84.2 - - - +
107E SER* 1.3 62.7 + - - +
109E ARG* 4.1 4.3 - - - +
110E SER* 3.2 20.3 + - - -
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Residues in contact with SER 107 (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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74D GLU 3.6 18.9 + - - -
75D GLY* 3.7 3.3 - - - -
76D ARG* 2.8 28.7 + - - +
104E ASP* 2.9 34.8 + - - -
106E ALA* 1.3 74.2 - - - +
108E LEU* 1.4 57.0 + - - +
110E SER* 3.0 3.7 + - - -
111E LEU* 2.8 36.4 + - - +
234E TRP* 4.9 5.6 - - - -
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Residues in contact with LEU 108 (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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67E ILE* 3.6 21.8 - - + -
70E LEU* 3.9 9.2 - - + -
102E VAL* 3.7 24.2 - - + -
104E ASP 3.2 8.9 + - - +
105E TYR 3.2 5.8 + - - +
107E SER* 1.4 75.0 - - - +
109E ARG* 1.4 64.1 + - - +
111E LEU* 3.3 11.1 + - + +
112E VAL* 3.0 48.6 + - + +
177E LEU* 5.2 0.4 - - + -
179E ILE* 3.7 22.2 - - + -
232E ILE* 4.0 18.2 - - + -
234E TRP* 3.7 26.5 - - + +
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Residues in contact with ARG 109 (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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65E THR* 5.7 0.2 - - - -
66E LEU* 3.8 9.0 - - + +
67E ILE* 3.7 19.6 - - + +
89E GLU* 2.5 47.3 + - - +
105E TYR* 2.9 33.6 + - + +
106E ALA* 4.1 4.7 - - - +
108E LEU* 1.4 74.7 - - - +
110E SER* 1.4 58.1 + - - +
113E ALA* 3.0 31.0 + - - +
267E ILE* 3.2 42.1 + - + +
269E ARG* 3.1 30.0 - - - +
67F GLU* 2.8 37.8 + - - -
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Residues in contact with SER 110 (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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75D GLY* 4.5 6.5 - - - -
76D ARG* 4.8 0.9 - - - -
79D ASP* 2.7 34.9 + - - -
106E ALA 3.2 12.1 + - - -
107E SER* 3.0 12.1 + - - -
109E ARG* 1.4 77.2 - - - +
111E LEU* 1.3 65.9 + - - +
113E ALA* 3.0 4.3 + - - +
114E SER* 2.9 26.7 + - - -
267E ILE* 5.9 1.1 - - - -
64F HIS* 2.9 20.5 + - - -
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Residues in contact with LEU 111 (chain E).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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73D VAL* 4.0 26.0 - - + +
74D GLU 4.7 0.2 - - - -
75D GLY* 4.6 9.9 - - - +
107E SER 2.8 26.7 + - - +
108E LEU* 3.8 9.4 - - + +
110E SER* 1.3 74.8 - - - +
112E VAL* 1.3 68.0 + - + +
114E SER* 4.2 5.0 - - - -
115E SER* 3.2 21.8 + - - -
177E LEU* 4.1 22.7 - - + -
234E TRP* 3.6 42.0 - - + -
236E ILE* 4.5 1.8 - - + -
260E MET* 3.8 26.6 - - + +
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Residues in contact with VAL 112 (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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66E LEU* 3.8 29.4 - - + -
67E ILE* 5.1 0.7 - - + -
70E LEU* 4.0 21.1 - - + -
84E TRP* 3.6 4.3 - - + -
108E LEU* 3.0 39.7 + - + +
109E ARG* 4.0 2.9 - - - +
111E LEU* 1.3 81.2 - - + +
113E ALA* 1.3 62.1 + - - +
115E SER* 3.0 18.9 + - - -
116E GLY 3.1 9.7 + - - -
117E THR 4.6 3.3 + - - +
118E LEU* 3.9 19.5 - - + -
177E LEU* 4.8 6.7 - - + -
260E MET* 5.4 0.9 - - - -
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Residues in contact with ALA 113 (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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66E LEU* 3.8 10.3 - - + -
84E TRP* 3.4 10.1 + - - +
109E ARG 3.0 21.0 + - - +
110E SER* 3.5 5.2 - - - +
112E VAL* 1.3 77.3 - - - +
114E SER* 1.3 59.0 + - - +
116E GLY 4.0 0.4 - - - -
265E SER* 3.2 26.0 - - - -
266E SER* 3.3 2.9 + - - -
267E ILE* 3.6 38.4 - - + +
64F HIS* 4.6 3.4 - - + -
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Residues in contact with SER 114 (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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110E SER* 2.9 17.2 + - - -
111E LEU* 4.3 4.5 - - - -
113E ALA* 1.3 72.0 - - - +
115E SER* 1.3 69.5 + - - +
116E GLY 3.1 2.0 + - - -
261E ARG 4.6 1.1 - - - +
263E GLY 4.1 13.7 + - - -
265E SER* 3.3 28.3 + - - -
64F HIS* 3.1 29.0 + - - -
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Residues in contact with SER 115 (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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111E LEU 3.2 12.3 + - - -
112E VAL* 3.0 12.5 + - - -
114E SER* 1.3 77.8 - - - +
116E GLY* 1.3 61.9 + - - +
117E THR* 3.4 9.0 + - - +
259E LYS 3.5 6.8 + - - -
260E MET* 3.3 20.2 - - - +
261E ARG* 2.8 62.3 + - - +
263E GLY* 5.0 1.7 + - - -
265E SER* 4.2 2.1 + - - -
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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