Contacts of the helix formed by residues 105 - 115 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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65C THR* 3.2 29.6 - - + +
67C ILE* 3.6 35.2 - - + +
100C TYR* 4.3 10.6 + + - -
102C VAL* 3.0 42.1 + - + +
104C ASP* 1.3 75.5 - - - +
106C ALA* 1.3 65.5 + - - +
108C LEU* 3.2 2.0 + - - +
109C ARG* 2.9 42.4 + - + +
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Residues in contact with ALA 106 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76B ARG* 3.8 36.1 - - + +
104C ASP* 3.6 10.5 - - - +
105C TYR* 1.3 82.9 - - - +
107C SER* 1.3 61.6 + - - +
109C ARG* 4.1 4.1 - - - +
110C SER* 3.2 21.3 + - - -
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Residues in contact with SER 107 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74B GLU 3.8 7.4 + - - -
75B GLY* 3.7 8.6 - - - -
76B ARG* 2.8 35.1 + - - +
104C ASP* 2.9 34.5 + - - -
106C ALA* 1.3 76.1 - - - +
108C LEU* 1.4 52.3 + - - +
110C SER* 3.0 3.7 + - - -
111C LEU* 2.8 41.1 + - - +
234C TRP* 4.9 5.4 - - - -
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Residues in contact with LEU 108 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67C ILE* 3.5 20.6 - - + -
70C LEU* 3.9 9.4 - - + -
71C LEU* 5.9 0.2 - - + -
102C VAL* 3.7 23.6 - - + -
104C ASP 3.2 9.0 + - - +
105C TYR 3.2 7.0 + - - +
107C SER* 1.4 76.6 - - - +
109C ARG* 1.3 63.8 + - - +
111C LEU* 3.2 11.1 + - + +
112C VAL* 3.0 47.7 + - + +
177C LEU* 5.2 0.2 - - + -
179C ILE* 3.7 21.8 - - + -
232C ILE* 4.0 17.5 - - + -
234C TRP* 3.7 27.4 - - + +
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Residues in contact with ARG 109 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66C LEU* 3.8 8.4 - - + +
67C ILE* 3.7 19.6 - - + +
89C GLU* 2.6 46.5 + - - +
105C TYR* 2.9 34.1 + - + +
106C ALA* 4.1 4.5 - - - +
108C LEU* 1.3 75.5 - - - +
110C SER* 1.4 57.7 + - - +
113C ALA* 3.0 32.1 + - - +
267C ILE* 3.2 43.9 + - + +
269C ARG* 3.0 29.8 - - - +
67D GLU* 2.9 38.0 + - - -
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Residues in contact with SER 110 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75B GLY* 4.6 4.5 - - - -
76B ARG* 4.8 1.6 - - - -
79B ASP* 2.7 35.1 + - - -
106C ALA 3.2 12.5 + - - -
107C SER* 3.0 12.1 + - - -
109C ARG* 1.4 78.5 - - - +
111C LEU* 1.4 65.4 + - - +
113C ALA* 3.1 4.7 + - - +
114C SER* 3.0 26.9 + - - -
267C ILE* 5.9 1.1 - - - -
64D HIS* 2.9 21.8 + - - -
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Residues in contact with LEU 111 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73B VAL* 4.1 24.2 - - + -
75B GLY* 4.5 10.8 - - - +
107C SER 2.8 26.2 + - - +
108C LEU* 3.8 9.9 - - + +
110C SER* 1.4 76.4 - - - +
112C VAL* 1.3 68.0 + - + +
114C SER* 4.1 5.0 - - - -
115C SER* 3.2 22.5 + - - -
177C LEU* 4.0 22.7 - - + -
234C TRP* 3.6 41.5 - - + -
236C ILE* 4.5 2.2 - - + -
260C MET* 3.8 25.2 - - + +
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Residues in contact with VAL 112 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66C LEU* 3.8 30.5 - - + -
67C ILE* 5.2 1.1 - - + -
70C LEU* 4.0 20.2 - - + -
84C TRP* 3.6 4.6 - - + -
108C LEU* 3.0 37.4 + - + +
109C ARG* 4.0 3.1 - - - +
111C LEU* 1.3 81.5 - - + +
113C ALA* 1.3 62.3 + - - +
115C SER* 3.0 18.6 + - - -
116C GLY 3.1 10.2 + - - -
117C THR 4.7 3.1 - - - +
118C LEU* 3.9 18.6 - - + -
177C LEU* 4.8 7.4 - - + -
260C MET* 5.4 0.9 - - - -
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Residues in contact with ALA 113 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66C LEU* 3.7 9.4 - - + +
84C TRP* 3.4 10.4 + - - -
109C ARG 3.0 21.6 + - - +
110C SER* 3.5 4.5 - - - +
112C VAL* 1.3 77.0 - - - +
114C SER* 1.3 57.9 + - - +
116C GLY 4.0 0.7 - - - -
265C SER* 3.2 25.8 - - - -
266C SER* 3.3 3.3 + - - -
267C ILE* 3.6 39.3 - - + +
64D HIS* 4.6 3.1 - - + -
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Residues in contact with SER 114 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79B ASP* 5.3 0.3 + - - -
110C SER* 3.0 11.2 + - - -
111C LEU* 4.3 4.3 - - - -
113C ALA* 1.3 72.9 - - - +
115C SER* 1.3 69.9 + - - +
116C GLY 3.1 2.4 + - - -
261C ARG 4.9 0.7 - - - -
262C THR* 5.9 0.2 - - - -
263C GLY 4.1 14.5 + - - +
265C SER* 3.3 27.6 + - - -
64D HIS* 3.1 35.2 + - - -
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Residues in contact with SER 115 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111C LEU 3.2 14.8 + - - -
112C VAL* 3.0 12.5 + - - -
114C SER* 1.3 76.5 - - - +
116C GLY* 1.3 62.3 + - - +
117C THR* 3.4 8.0 + - - +
259C LYS 3.5 6.6 + - - -
260C MET* 3.3 20.2 - - - +
261C ARG* 2.8 61.6 + - - +
263C GLY* 5.0 1.6 + - - -
265C 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