Contacts of the helix formed by residues 101 - 110 (chain K) in PDB entry 3EXG
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 SER 101 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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96K PHE* 5.1 1.3 - - - -
100K LEU* 1.3 75.9 - - - +
102K VAL* 1.3 66.3 + - - +
103K ARG* 2.9 14.1 + - - +
104K GLU* 2.7 41.9 + - - +
105K ILE* 3.1 23.0 + - - +
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Residues in contact with VAL 102 (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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41K THR* 3.8 16.4 - - + -
45K MET* 3.3 34.3 - - + -
96K PHE* 3.8 23.5 - - + -
100K LEU 4.2 0.6 + - - -
101K SER* 1.3 72.6 - - - +
103K ARG* 1.3 55.0 + - - +
105K ILE* 3.4 1.7 + - - +
106K LEU* 2.9 33.7 + - + +
316K GLU* 5.1 10.3 - - + +
317K ILE* 3.8 23.6 - - + -
320K ALA* 3.6 20.2 - - + -
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Residues in contact with ARG 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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101K SER* 2.9 12.2 + - - +
102K VAL* 1.3 73.3 - - - +
104K GLU* 1.3 61.6 + - - +
105K ILE 3.1 1.5 + - - -
106K LEU* 3.2 2.1 + - - +
107K ALA* 2.9 31.7 + - - +
319K ASP* 4.3 13.9 + - - +
320K ALA* 4.0 21.4 - - + +
322K GLN* 5.8 2.0 - - - +
323K PHE* 3.3 61.9 - - + +
324K ALA* 4.8 0.5 - - - +
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Residues in contact with GLU 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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100K LEU* 3.4 21.5 - - + +
101K SER* 2.7 36.2 + - - +
103K ARG* 1.3 75.3 - - - +
105K ILE* 1.3 59.7 + - - +
108K GLU* 3.2 18.2 + - - +
114K GLY 3.8 18.6 - - - +
115K GLY* 4.1 0.7 - - - -
116K CYS* 3.1 49.7 + - - +
323K PHE* 4.9 0.6 - - - -
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Residues in contact with ILE 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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45K MET* 3.3 38.6 - - + -
92K HIS* 4.1 9.6 - - + +
95K THR* 3.4 35.7 - - + -
96K PHE* 3.6 21.1 - - + +
100K LEU* 4.1 7.9 - - + -
101K SER 3.1 16.0 + - - +
103K ARG 3.1 1.2 - - - -
104K GLU* 1.3 77.5 - - - +
106K LEU* 1.3 67.7 + - + +
108K GLU* 3.4 3.8 + - - +
109K LEU* 3.3 27.1 + - + +
116K CYS* 4.9 0.2 - - - -
126K MET* 4.0 21.7 - - + +
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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
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45K MET* 4.3 16.4 - - + +
48K LYS* 3.9 26.2 - - + -
49K ALA* 4.2 19.7 - - + -
52K LEU* 4.3 10.5 - - + -
102K VAL* 2.9 37.4 + - + +
103K ARG 4.2 1.3 - - - +
105K ILE* 1.3 70.6 - - + +
107K ALA* 1.3 60.7 + - - +
109K LEU* 2.9 41.5 + - + +
110K THR* 2.9 16.3 + - - +
317K ILE* 4.9 2.2 - - + +
320K ALA* 4.4 2.7 - - + +
321K ALA* 4.2 17.7 - - + +
324K ALA* 3.6 15.8 - - + +
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Residues in contact with ALA 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 ARG 2.9 17.8 + - - +
106K LEU* 1.3 76.5 - - - +
108K GLU* 1.3 61.8 + - - +
110K THR* 3.4 8.9 + - - -
111K GLY 3.2 4.5 + - - -
112K ARG* 3.1 30.2 + - + +
114K GLY* 3.6 9.2 - - - +
115K GLY* 3.5 23.3 - - - +
323K PHE* 3.9 15.5 - - + -
324K ALA* 3.4 9.9 - - + +
327K ASP* 5.4 0.2 - - - +
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Residues in contact with GLU 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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304J TYR* 3.4 12.6 - - - -
104K GLU 3.2 21.7 + - - +
105K ILE 3.9 3.8 - - - +
106K LEU 3.2 0.4 - - - -
107K ALA* 1.3 76.5 - - - +
109K LEU* 1.3 62.2 + - - +
111K GLY* 3.3 8.5 + - - -
112K ARG 5.1 0.4 - - - +
115K GLY* 3.4 4.8 - - - -
116K CYS* 3.9 14.8 - - - -
117K ALA* 2.4 49.9 + - + -
118K LYS 3.3 2.1 + - - -
119K GLY* 3.2 18.0 + - - -
121K GLY 3.1 10.1 + - - -
122K GLY* 2.9 39.4 + - - +
125K HIS 5.1 0.7 - - - +
126K MET* 4.4 7.4 - - + -
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Residues in contact with LEU 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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304J TYR* 2.6 29.0 + - - -
49K ALA* 4.2 10.3 - - + -
58K ILE* 3.6 34.2 - - + +
62K CYS* 4.9 1.8 - - - -
92K HIS* 4.1 19.5 - - + +
105K ILE* 3.3 18.8 - - + +
106K LEU* 2.9 30.6 + - + +
108K GLU* 1.3 78.8 - - - +
110K THR* 1.3 58.0 + - - +
111K GLY 3.1 2.0 + - - -
122K GLY 4.5 0.7 - - - -
123K SER* 3.4 42.6 - - - +
126K MET* 5.1 3.8 - - - -
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Residues in contact with THR 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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304J TYR* 4.7 0.7 - - - -
52K LEU* 4.4 14.4 - - + -
57K ILE* 3.4 45.6 - - + +
58K ILE* 4.0 11.9 - - + -
106K LEU 2.9 16.4 + - - +
107K ALA 3.4 6.1 + - - -
109K LEU* 1.3 73.3 - - - +
111K GLY* 1.3 54.7 + - - +
112K ARG* 2.7 32.9 + - - +
324K ALA* 3.2 31.1 + - + +
325K THR* 4.6 2.9 - - + -
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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