Contacts of the helix formed by residues 99 - 112 (chain H) in PDB entry 5L08
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 99 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28H ASP* 4.9 7.2 + - - -
96H ALA* 5.8 1.3 - - - -
97H GLN 3.8 4.4 + - - -
98H ILE* 1.3 75.7 - - - +
100H ALA* 1.3 59.7 + - - +
101H TYR* 3.0 24.0 + - - +
102H ARG* 2.9 29.5 + - - +
103H VAL* 3.1 9.2 + - - +
154H GLU* 4.0 11.2 + - - -
181H PHE* 4.4 8.3 - - - -
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Residues in contact with ALA 100 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96H ALA* 6.2 0.4 - - - +
98H ILE 3.5 2.2 + - - -
99H SER* 1.3 72.1 + - - +
101H TYR* 1.3 53.4 + - - +
103H VAL* 3.5 14.0 - - + +
104H MET* 2.8 43.7 + - + +
180H GLU* 3.3 31.4 - - - +
181H PHE* 3.9 13.5 - - + -
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Residues in contact with TYR 101 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28H ASP* 5.6 0.7 - - - -
99H SER* 3.2 15.7 + - - +
100H ALA* 1.3 77.7 - - - +
102H ARG* 1.3 91.5 + - + +
104H MET* 3.5 12.2 + - + +
105H LEU* 3.2 47.3 + - + +
147H GLU* 4.4 6.7 + - - +
152H LEU* 3.5 15.4 + - - +
153H GLY* 3.2 47.6 + - - -
154H GLU* 3.6 33.2 - - + -
157H LEU* 3.9 26.7 - - + -
178H TYR* 5.3 2.0 - + + -
181H PHE* 4.3 6.5 - - + -
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Residues in contact with ARG 102 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24H PHE* 3.6 36.2 - - + -
25H LEU* 4.3 13.5 - - + +
27H LEU* 3.6 27.3 - - - +
28H ASP* 3.0 42.4 + - - +
98H ILE* 4.0 17.5 - - + -
99H SER* 2.9 15.6 + - - +
101H TYR* 1.3 95.7 - - + +
103H VAL* 1.3 60.7 + - - +
105H LEU* 3.5 1.4 + - - +
106H TYR* 3.0 29.9 + - - +
147H GLU* 2.7 42.4 + - - -
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Residues in contact with VAL 103 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67H PHE* 6.3 3.4 - - + -
68H ARG* 3.4 49.4 - - + +
98H ILE* 4.1 2.7 - - + +
99H SER 3.1 13.6 + - - +
100H ALA* 3.2 15.2 + - + +
102H ARG* 1.3 78.5 - - - +
104H MET* 1.3 60.9 + - + +
106H TYR* 3.3 11.2 + - + +
107H GLN* 2.8 30.3 + - + +
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Residues in contact with MET 104 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100H ALA* 2.8 37.9 + - + +
101H TYR* 3.8 10.3 - - - +
103H VAL* 1.3 76.1 - - + +
105H LEU* 1.3 59.0 + - + +
107H GLN* 3.1 8.3 + - - +
108H ILE* 2.8 37.9 + - + +
157H LEU* 4.1 11.7 - - + -
174H ILE* 3.9 16.1 - - + +
175H ILE* 4.3 4.3 - - - +
177H ASP* 3.6 21.5 - - + +
178H TYR* 3.5 52.7 - - + -
180H GLU* 5.4 2.0 - - - +
181H PHE* 4.0 7.6 - - + -
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Residues in contact with LEU 105 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24H PHE* 3.7 30.1 - - + -
101H TYR* 3.2 53.0 + - + +
102H ARG* 3.8 4.0 - - - +
104H MET* 1.3 78.4 - - + +
106H TYR* 1.3 62.9 + - - +
108H ILE* 3.3 9.0 + - + +
109H SER 3.1 16.3 + - - -
140H LEU* 3.8 4.4 - - - +
143H PHE* 3.4 31.0 - - + -
147H GLU* 4.9 0.2 - - - +
152H LEU* 4.5 7.9 - - + -
157H LEU* 4.0 10.3 - - + -
160H LEU* 3.6 30.7 - - + -
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Residues in contact with TYR 106 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18H ASP* 5.5 2.9 + - - -
21H SER* 3.6 34.2 + - - -
24H PHE* 4.9 2.2 - + + -
25H LEU* 4.7 15.5 - - + -
68H ARG* 2.9 33.1 + - + -
69H ILE* 3.5 18.6 + - + +
70H ASN* 4.3 9.0 + - - -
102H ARG 3.0 14.9 + - - +
103H VAL* 3.4 13.9 - - + +
105H LEU* 1.3 74.1 - - - +
107H GLN* 1.3 73.8 + - + +
109H SER* 2.6 28.4 + - - -
110H GLU* 3.0 42.9 + - + +
140H LEU* 4.0 12.0 - - + +
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Residues in contact with GLN 107 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129F SER* 4.9 14.8 + - - -
130F LYS* 5.8 2.8 - - - +
103H VAL* 2.8 21.6 + - + +
104H MET* 3.5 11.4 - - - +
106H TYR* 1.3 81.8 - - - +
108H ILE* 1.3 57.7 + - - +
110H GLU* 3.2 15.8 + - - +
111H GLU* 2.9 33.2 + - - +
174H ILE* 4.1 23.9 - - + +
177H ASP* 6.2 0.2 - - - +
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Residues in contact with ILE 108 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104H MET* 2.8 22.0 + - + +
105H LEU* 3.4 18.2 - - + +
106H TYR 3.1 0.2 - - - -
107H GLN* 1.3 76.7 - - - +
109H SER* 1.3 58.6 + - - +
111H GLU* 3.0 3.3 + - - +
112H VAL* 2.8 41.0 + - + +
120H PHE* 6.2 0.2 - - + -
139H LEU* 3.7 20.6 - - + -
143H PHE* 4.0 6.3 - - + -
157H LEU* 5.4 1.6 - - + -
160H LEU* 4.0 26.9 - - + -
164H CYS* 5.3 6.3 - - - -
171H LEU* 4.1 12.1 - - + +
174H ILE* 3.6 25.6 - - + -
175H ILE* 4.0 19.1 - - + -
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Residues in contact with SER 109 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132F LYS* 2.8 21.8 + - - -
105H LEU 3.1 2.2 + - - -
106H TYR* 2.6 24.2 + - - -
108H ILE* 1.3 79.0 - - - +
110H GLU* 1.3 64.8 + - - +
112H VAL* 3.5 5.5 - - - +
138H ASN* 4.9 2.5 - - - -
139H LEU* 3.8 24.2 - - - +
140H LEU* 3.6 37.7 - - - +
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Residues in contact with GLU 110 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130F LYS 4.9 7.7 - - - +
131F CYS 5.4 0.3 - - - +
132F LYS* 3.1 56.9 + - + +
133F LEU 5.4 0.7 + - - -
149F ARG* 5.1 3.1 + - - -
70H ASN* 5.3 3.4 + - - +
106H TYR* 3.0 60.2 + - + +
107H GLN* 3.4 19.7 - - - +
108H ILE 3.1 0.2 - - - -
109H SER* 1.3 82.2 + - - +
111H GLU* 1.3 59.8 + - - +
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Residues in contact with GLU 111 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125F GLN* 5.6 1.2 - - - +
129F SER* 5.1 14.2 - - - +
107H GLN* 2.9 18.5 + - - +
108H ILE 3.0 2.7 + - - +
110H GLU* 1.3 76.8 - - - +
112H VAL* 1.3 63.2 + - - +
113H SER* 3.4 2.9 + - - -
116H GLU* 3.8 4.3 - - - +
168H ASN* 4.3 8.0 + - - +
170H SER* 2.9 27.6 + - - +
171H LEU* 3.4 27.8 - - + -
174H ILE* 3.7 14.1 - - + -
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Residues in contact with VAL 112 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132F LYS* 2.6 29.5 + - - -
108H ILE* 2.8 26.6 + - + +
109H SER 3.5 3.1 + - - +
110H GLU 3.5 0.2 - - - -
111H GLU* 1.3 69.6 - - - +
113H SER* 1.3 74.8 + - - +
114H ARG 4.0 0.2 + - - -
116H GLU* 3.4 11.9 - - + -
117H LEU* 3.7 19.7 - - + +
120H PHE* 3.8 12.8 - - + -
139H LEU* 3.6 26.5 - - + -
171H LEU* 3.4 29.6 - - + -
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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