Contacts of the helix formed by residues 102 - 113 (chain K) in PDB entry 5A15
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 GLU 102 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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81K LEU* 3.4 11.4 - - + +
100K PHE* 3.1 29.2 - - + -
101K PRO* 1.3 96.3 - - + +
103K LYS* 1.3 63.5 + - - +
104K GLY 3.3 3.4 - - - +
105K ARG* 3.3 29.1 + - + -
106K LEU* 3.2 15.6 + - - +
83L ARG* 2.8 44.6 + - - -
84L TYR* 4.3 0.5 + - - -
96L LEU 5.7 0.2 - - - -
97L PRO* 3.7 19.7 - - + +
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Residues in contact with LYS 103 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96K LEU* 4.7 11.2 - - + -
100K PHE* 3.7 19.5 + - + +
101K PRO 3.7 2.4 + - - -
102K GLU* 1.3 77.5 - - - +
104K GLY* 1.3 62.5 + - - +
106K LEU* 3.4 5.9 + - - +
107K LYS* 3.2 21.0 + - - +
122K LEU* 4.4 19.7 - - + +
98L ASP* 4.4 6.1 + - - +
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Residues in contact with GLY 104 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102K GLU* 3.3 1.0 - - - +
103K LYS* 1.3 80.2 - - - +
105K ARG* 1.3 60.2 + - - +
107K LYS* 3.3 12.5 - - - +
108K ARG* 3.3 16.5 + - - +
95L VAL* 3.8 20.7 - - - +
98L ASP* 5.4 3.8 + - - -
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Residues in contact with ARG 105 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78K ASP* 3.7 6.7 + - - +
81K LEU* 3.6 20.5 - - + +
102K GLU* 3.3 29.1 + - + +
103K LYS 3.3 0.4 - - - -
104K GLY* 1.3 73.7 - - - +
106K LEU* 1.3 67.2 + - - +
108K ARG* 3.0 16.7 + - - +
109K GLU* 3.0 19.0 + - - +
83L ARG* 2.9 44.5 - - - +
84L TYR* 4.2 13.2 - - - -
87L ASP* 2.2 38.4 + - - +
95L VAL* 3.1 40.2 + - + +
96L LEU 4.2 4.5 - - - +
97L PRO* 4.3 11.2 - - - -
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Residues in contact with LEU 106 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81K LEU* 3.8 32.0 - - + +
84K TYR* 3.8 29.8 - - + -
85K ILE* 4.0 19.1 - - + +
94K VAL* 5.4 1.8 - - + -
96K LEU* 4.4 14.8 - - + -
100K PHE* 4.6 7.4 - - + -
102K GLU 3.2 15.1 + - - +
103K LYS 3.7 5.4 - - - +
105K ARG* 1.3 79.7 - - - +
107K LYS* 1.3 56.3 + - - +
109K GLU* 3.2 8.5 + - + +
110K ALA* 2.8 27.9 + - - +
118K LEU* 5.2 5.2 - - + -
122K LEU* 3.5 27.4 - - + -
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Residues in contact with LYS 107 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103K LYS 3.2 12.9 + - - +
104K GLY* 3.3 14.6 - - - +
105K ARG 3.1 0.4 - - - -
106K LEU* 1.3 76.1 - - - +
108K ARG* 1.3 57.6 + - - +
110K ALA* 3.2 5.1 + - - +
111K GLU* 3.0 49.0 + - - +
119K VAL* 4.3 11.9 - - + -
122K LEU* 3.6 21.4 - - + +
123K THR* 3.3 38.3 - - + +
124K PRO* 6.0 1.0 - - + +
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Residues in contact with ARG 108 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77K ARG* 3.9 11.7 - - - +
104K GLY 3.3 8.3 + - - +
105K ARG* 3.0 13.7 + - - +
107K LYS* 1.3 79.7 - - - +
109K GLU* 1.3 64.6 + - - +
111K GLU* 3.2 38.1 + - - +
112K TYR* 3.1 36.6 + - - +
91L ASP* 3.3 38.5 + - - +
93L GLN* 4.7 24.8 - - + +
95L VAL* 4.6 15.5 - - + -
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Residues in contact with GLU 109 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77K ARG* 2.8 54.3 + - - +
78K ASP* 4.2 16.6 + - - +
81K LEU* 3.8 27.7 - - + +
85K ILE* 4.2 16.8 - - + -
105K ARG* 3.0 19.3 + - - +
106K LEU* 3.2 8.7 + - + +
108K ARG* 1.3 75.0 - - - +
110K ALA* 1.3 60.2 + - - +
112K TYR* 3.2 2.1 + - - +
113K PHE* 2.9 43.4 + - + -
87L ASP* 4.5 6.2 - - - +
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Residues in contact with ALA 110 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85K ILE* 3.9 9.1 - - - +
106K LEU 2.8 14.5 + - - +
107K LYS* 3.2 13.0 + - - +
109K GLU* 1.3 77.4 - - - +
111K GLU* 1.3 55.7 + - - +
113K PHE* 3.5 2.0 + - - -
114K GLN 2.9 22.5 + - - -
115K LEU* 3.0 14.6 + - - +
118K LEU* 3.7 30.1 - - + -
119K VAL* 3.6 18.6 - - + +
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Residues in contact with GLU 111 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107K LYS* 3.0 43.2 + - - +
108K ARG* 3.2 36.8 + - - +
109K GLU 3.2 0.2 - - - -
110K ALA* 1.3 73.9 - - - +
112K TYR* 1.3 66.1 + - - +
114K GLN* 3.1 19.5 + - - +
119K VAL* 3.9 20.5 - - + +
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Residues in contact with TYR 112 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50K LEU* 3.5 37.5 - - + +
75K ILE* 4.8 5.9 - - + +
76K ASP* 4.9 4.0 + - - +
77K ARG* 3.4 60.5 - - + +
108K ARG* 3.1 26.5 + - - +
109K GLU 3.2 7.4 + - - +
111K GLU* 1.3 78.9 - - - +
113K PHE* 1.3 78.7 + + - +
114K GLN* 3.3 11.3 + - - +
39L ARG* 4.4 20.7 + - - -
91L ASP* 5.2 0.2 - - - -
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Residues in contact with PHE 113 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49K SER* 3.9 2.3 - - - -
50K LEU* 3.3 27.9 + - + -
51K LEU* 4.1 28.8 + - + -
54K MET* 6.1 0.7 - - - -
75K ILE* 4.0 22.9 - - + -
77K ARG* 4.2 4.7 - - + -
82K PHE* 3.6 37.9 - + - -
85K ILE* 3.9 20.2 - - + -
109K GLU* 2.9 45.9 + - + +
110K ALA 4.2 2.5 - - - +
112K TYR* 1.3 93.2 - + - +
114K GLN* 1.3 73.9 + - - +
115K LEU* 3.6 20.2 - - + +
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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