Contacts of the helix formed by residues 102 - 112 (chain S) in PDB entry 2DFS
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 ALA 102 (chain S).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100S ILE 3.9 0.4 + - - -
101S SER* 1.3 72.5 - - - +
103S ALA* 1.4 55.7 + - - +
105S LEU* 3.5 13.5 + - + +
106S ARG* 3.0 31.2 + - - +
121S VAL* 5.9 0.3 - - - +
125S ILE* 6.0 6.7 - - + -
130S ILE* 4.0 17.4 - - + +
134S GLY* 3.1 18.0 + - - +
135S GLN* 4.7 0.4 - - - +
136S VAL* 4.8 2.6 - - + +
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Residues in contact with ALA 103 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101S SER* 3.5 10.9 + - - +
102S ALA* 1.4 77.3 - - - +
104S GLU* 1.3 57.1 + - + +
106S ARG* 3.3 7.5 + - - +
107S HIS* 2.9 28.9 + - - +
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Residues in contact with GLU 104 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92S PHE* 3.4 52.8 - - + +
100S ILE* 3.8 7.8 - - + +
101S SER* 2.6 48.1 + - - +
103S ALA* 1.3 75.5 - - + +
105S LEU* 1.3 57.2 + - - +
107S HIS* 3.4 6.4 + - - +
108S VAL* 3.1 28.9 + - - +
135S GLN* 5.7 0.5 + - - -
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Residues in contact with LEU 105 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
897M TYR* 3.9 19.5 - - - +
90S ARG* 3.5 27.6 - - - +
100S ILE* 4.0 12.2 - - + +
101S SER 3.0 15.3 + - - +
102S ALA* 3.6 9.2 - - + +
103S ALA 3.4 0.2 - - - -
104S GLU* 1.3 72.4 - - - +
106S ARG* 1.3 62.9 + - - +
108S VAL* 3.3 10.1 - - + +
109S MET* 3.2 28.4 + - + +
121S VAL* 5.5 5.8 - - + -
124S MET* 6.2 0.2 - - + -
125S ILE* 4.6 17.3 - - + -
136S VAL* 4.5 16.2 - - + -
141S PHE* 3.8 29.8 - - + -
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Residues in contact with ARG 106 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102S ALA 3.0 17.8 + - - +
103S ALA* 3.3 7.2 + - - +
105S LEU* 1.3 72.5 - - - +
107S HIS* 1.4 60.3 + - - +
109S MET* 3.3 2.1 + - - -
110S THR* 2.8 45.1 + - + +
118S ASP* 2.7 47.0 + - - +
121S VAL* 3.9 24.6 - - + +
122S ASP* 2.6 45.4 + - - -
125S ILE* 3.7 15.2 - - - +
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Residues in contact with HIS 107 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21R LYS* 2.7 48.5 + - + +
92S PHE* 3.2 38.7 - + - -
103S ALA 2.9 16.9 + - - +
104S GLU* 3.7 6.1 - - - +
105S LEU 3.4 0.2 - - - -
106S ARG* 1.4 74.2 - - - +
108S VAL* 1.3 57.2 + - - +
110S THR* 4.3 4.5 - - - -
111S ASN* 2.8 50.5 + - + +
112S LEU* 3.8 22.4 - - + +
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Residues in contact with VAL 108 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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890M ILE* 3.9 20.5 - - + +
894M GLN* 4.0 2.4 + - - -
89S PHE* 3.2 40.8 - - + -
90S ARG* 5.2 4.0 - - - +
91S VAL* 6.0 0.2 - - + -
92S PHE* 3.8 18.2 - - + -
100S ILE* 5.5 2.0 - - + -
104S GLU 3.1 12.7 + - - +
105S LEU* 3.3 24.7 - - + +
107S HIS* 1.3 82.8 - - - +
109S MET* 1.3 67.7 + - + +
112S LEU* 3.3 29.5 + - + +
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Residues in contact with MET 109 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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890M ILE* 4.3 3.1 - - + +
893M LEU* 4.2 9.6 - - + -
894M GLN* 3.0 33.8 + - + +
897M TYR* 3.5 41.1 - - + +
89S PHE* 4.1 26.7 - - + -
90S ARG* 5.9 1.1 - - - +
105S LEU* 3.2 23.5 + - + +
106S ARG 3.9 2.0 - - - +
108S VAL* 1.3 87.9 - - + +
110S THR* 1.3 59.8 + - - +
115S LYS* 3.7 0.5 - - - -
116S LEU* 2.9 37.1 + - + +
121S VAL* 3.9 19.7 - - + -
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Residues in contact with THR 110 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106S ARG* 2.8 34.4 + - + +
107S HIS* 4.2 2.9 + - - -
109S MET* 1.3 73.3 - - - +
111S ASN* 1.4 59.1 + - - +
112S LEU 3.7 0.2 - - - -
115S LYS* 3.4 23.7 - - - +
116S LEU 3.3 22.4 - - - +
117S THR 3.9 9.4 - - - +
118S ASP* 4.1 17.6 + - - +
121S VAL* 3.7 24.2 - - + -
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Residues in contact with ASN 111 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17R SER* 3.7 9.9 + - - +
18R LEU* 4.3 1.0 - - - +
20R ASP* 3.3 26.3 + - - -
21R LYS* 4.1 5.3 - - - +
22R ASP 4.4 1.8 - - - +
23R GLY* 4.6 9.8 - - - +
107S HIS* 2.8 41.6 + - + +
110S THR* 1.4 75.1 + - - +
112S LEU* 1.3 64.7 + - - +
115S LYS* 2.7 47.5 + - - +
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Residues in contact with LEU 112 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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887M LEU* 4.9 4.5 - - + -
890M ILE* 3.6 31.2 - - + -
894M GLN* 2.8 29.1 + - - -
17R SER 4.0 2.9 - - - +
18R LEU* 3.6 42.0 - - + +
21R LYS* 5.5 1.8 - - + -
91S VAL* 5.9 3.6 - - + -
92S PHE* 4.8 5.6 - - + -
107S HIS* 3.8 33.0 - - + +
108S VAL* 3.3 22.2 + - + +
111S ASN* 1.3 89.6 - - - +
113S GLY* 1.4 59.6 + - - +
115S LYS* 3.5 6.8 + - - -
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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