Contacts of the helix formed by residues 100 - 114 (chain C) in PDB entry 4DHJ
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 GLN 100 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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128A PRO* 4.9 10.1 - - - +
129A ASP* 5.5 0.8 + - - +
130A TRP* 3.0 38.8 + - + +
131A THR* 4.0 12.7 + - + +
7C ARG* 3.8 6.3 - - - +
11C GLU* 3.3 16.9 - - - +
14C ARG* 5.2 2.1 - - - +
18C GLU* 5.0 0.5 - - - +
62C TYR* 3.8 4.3 - - - -
95C TRP* 3.8 5.0 - - - -
99C LEU* 1.3 78.6 - - - +
101C ILE* 1.3 67.9 + - - +
102C ARG* 2.9 48.7 + - + +
103C THR* 3.1 30.5 + - - +
104C VAL* 3.4 9.7 + - - +
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Residues in contact with ILE 101 (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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11C GLU* 2.6 32.9 + - + +
15C LEU* 3.9 34.8 - - + -
35C PHE* 4.2 6.1 - - + -
37C VAL* 5.9 0.4 - - + -
56C LEU* 3.8 28.7 - - + -
58C LEU* 3.9 37.5 - - + -
62C TYR* 3.7 2.8 + - - +
67C PRO* 4.9 4.3 - - + -
100C GLN* 1.3 71.2 - - - +
102C ARG* 1.3 64.3 + - - +
104C VAL* 3.0 9.7 + - - +
105C LEU* 3.0 43.2 + - + +
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Residues in contact with ARG 102 (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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128A PRO* 5.8 2.6 - - - +
129A ASP* 5.1 5.7 + - - -
130A TRP* 4.0 8.9 - - - +
11C GLU* 4.5 0.4 + - - -
15C LEU* 5.2 9.2 - - + +
18C GLU* 2.9 46.7 + - - +
20C VAL* 4.7 17.5 - - + -
100C GLN* 2.9 50.0 + - + +
101C ILE* 1.3 81.5 - - - +
103C THR* 1.3 56.8 + - - +
105C LEU* 3.3 6.4 + - - +
106C LEU* 2.8 55.6 + - + +
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Residues in contact with THR 103 (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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90C ILE* 4.1 15.0 - - + -
99C LEU* 4.1 25.1 - - + +
100C GLN* 3.1 35.9 + - - +
102C ARG* 1.3 80.5 + - - +
104C VAL* 1.3 58.3 + - - +
106C LEU* 3.9 7.6 - - - +
107C SER* 2.9 31.0 + - - -
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Residues in contact with VAL 104 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56C LEU* 5.2 1.3 - - + -
67C PRO* 4.3 7.2 - - + -
69C VAL* 3.9 12.3 - - + -
88C LEU* 4.6 1.7 - - + +
90C ILE* 3.9 19.5 - - + -
91C LEU* 3.7 33.4 - - + -
95C TRP* 3.9 29.4 - - + -
100C GLN 3.4 3.1 + - - +
101C ILE* 3.0 9.8 + - - +
103C THR* 1.3 75.8 - - - +
105C LEU* 1.3 62.8 + - + +
107C SER* 3.1 3.1 + - - -
108C ILE* 2.8 47.1 + - + +
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Residues in contact with LEU 105 (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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15C LEU* 4.8 3.8 - - + -
23C ILE* 3.7 29.2 - - + +
25C ALA* 4.3 8.7 - - + -
37C VAL* 3.9 39.0 - - + -
39C ILE* 4.1 3.9 - - + +
54C LEU* 4.9 5.6 - - + -
56C LEU* 4.2 18.8 - - + -
69C VAL* 4.9 2.2 - - + -
101C ILE* 3.0 35.9 + - + +
102C ARG* 3.8 5.8 - - - +
104C VAL* 1.3 80.8 - - + +
106C LEU* 1.3 63.4 - - - +
108C ILE* 3.2 14.4 + - + +
109C GLN* 3.0 22.9 + - - +
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Residues in contact with LEU 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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20C VAL* 3.9 22.7 - - + -
23C ILE* 4.2 4.0 - - + -
102C ARG* 2.8 45.4 + - + +
103C THR* 3.9 6.3 - - - +
105C LEU* 1.3 76.0 - - - +
107C SER* 1.3 57.6 + - - +
109C GLN* 3.4 22.9 + - - +
110C ALA* 3.0 27.5 + - - +
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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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88C LEU* 3.7 25.5 - - - +
89C ASP* 5.2 0.3 + - - -
90C ILE* 3.8 15.9 - - - +
103C THR* 2.9 19.9 + - - -
104C VAL 3.7 3.6 - - - -
106C LEU* 1.3 75.8 - - - +
108C ILE* 1.3 64.2 + - - +
110C ALA* 3.3 7.1 + - - +
111C LEU* 3.0 24.6 + - - +
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Residues in contact with ILE 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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39C ILE* 3.8 17.5 - - + -
54C LEU* 3.8 12.6 - - + -
69C VAL* 4.0 5.8 - - + -
71C PHE* 3.9 28.7 - - + -
86C ILE* 3.7 30.3 - - + -
88C LEU* 4.1 16.6 - - + -
91C LEU* 4.9 0.7 - - + -
104C VAL* 2.8 36.8 + - + +
105C LEU* 3.2 7.8 + - + +
107C SER* 1.3 72.8 - - - +
109C GLN* 1.3 67.3 + - - +
111C LEU* 3.1 20.4 + - + +
112C LEU* 3.1 15.0 + - + +
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Residues in contact with GLN 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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21C PRO 3.0 26.1 + - - +
22C GLY* 3.9 10.5 + - - -
23C ILE* 3.7 24.3 - - + +
39C ILE* 4.3 19.0 - - + +
40C ALA 4.9 4.0 + - - -
42C PRO* 4.1 16.4 - - + +
105C LEU 3.0 12.7 + - - +
106C LEU* 3.5 22.1 - - - +
107C SER 3.4 0.2 - - - -
108C ILE* 1.3 78.5 - - - +
110C ALA* 1.3 61.5 + - - +
112C LEU* 3.2 17.2 + - - +
113C SER* 3.5 8.0 + - - -
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Residues in contact with ALA 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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106C LEU 3.0 17.3 + - - +
107C SER* 3.8 7.2 - - - +
108C ILE 3.3 0.4 - - - -
109C GLN* 1.3 73.8 - - - +
111C LEU* 1.3 60.4 + - - +
113C SER* 3.2 9.6 + - - -
114C ALA* 2.9 30.3 + - - +
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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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77C HIS* 2.8 29.2 + - + +
79C ASN* 4.0 35.7 - - + +
80C VAL* 6.1 1.6 - - + -
86C ILE* 4.7 8.3 - - + -
87C CYS 4.2 1.6 - - - +
88C LEU* 4.0 32.3 - - + -
107C SER* 3.0 13.0 + - - +
108C ILE* 3.1 20.4 + - + +
110C ALA* 1.3 76.2 - - - +
112C LEU* 1.3 61.5 + - + +
114C ALA 3.4 9.2 - - - +
115C PRO* 3.3 15.8 - - - +
117C PRO* 5.7 6.3 - - + -
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Residues in contact with LEU 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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39C ILE* 4.3 22.2 - - + -
40C ALA 4.6 0.2 - - - +
42C PRO* 3.9 25.4 - - + -
45C SER* 3.8 5.0 - - - -
47C PHE* 3.3 27.5 - - + -
52C PHE* 4.4 21.5 - - + -
71C PHE* 4.2 18.4 - - + -
75C ILE* 3.5 27.8 - - + -
77C HIS* 3.7 18.4 - - + +
80C VAL* 5.8 0.4 - - + -
108C ILE* 3.1 18.3 + - + +
109C GLN 3.2 8.5 + - - +
111C LEU* 1.3 77.2 - - + +
113C SER* 1.3 60.4 + - - +
115C PRO* 3.6 6.6 - - - +
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Residues in contact with SER 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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42C PRO* 3.6 21.5 - - - +
43C GLN 4.7 4.7 + - - -
44C ASP 5.4 2.8 + - - +
45C SER* 4.6 9.7 - - - -
109C GLN 3.5 7.3 + - - -
110C ALA* 3.2 12.2 + - - -
112C LEU* 1.3 78.7 - - - +
114C ALA* 1.3 58.6 + - - +
115C PRO* 3.4 8.8 - - - +
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Residues in contact with ALA 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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110C ALA 2.9 13.4 + - - +
111C LEU* 3.4 15.0 - - - +
113C SER* 1.3 79.9 - - - +
115C PRO* 1.4 63.5 - - - +
116C ASN 3.3 9.3 + - - +
117C PRO* 4.8 2.6 - - - +
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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