Contacts of the helix formed by residues 98 - 112 (chain C) in PDB entry 4DDG
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 THR 98 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1131B THR* 3.4 35.9 - - + +
1133B PHE* 4.7 11.2 - - + -
1134B THR* 4.4 6.5 - - + -
9C GLU* 3.5 12.6 - - - -
12C ASP* 4.6 3.3 + - - +
93C TRP* 4.9 1.8 - - - -
96C ALA 4.4 0.7 - - - +
97C LEU* 1.3 78.2 - - - +
99C ILE* 1.3 62.3 + - - +
100C SER* 2.8 24.0 + - - -
101C LYS* 3.0 34.4 + - + +
102C VAL* 3.3 15.7 + - - +
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Residues in contact with ILE 99 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9C GLU* 2.6 26.4 + - + +
13C LEU* 4.7 11.7 - - + -
33C TRP* 4.0 25.4 - - + -
54C ILE* 3.7 33.9 - - + -
56C PHE* 3.8 26.7 - - + -
60C TYR* 4.4 2.3 + - - +
65C PRO* 4.3 15.5 - - + -
67C VAL* 5.0 1.8 - - + -
98C THR* 1.3 71.6 - - - +
100C SER* 1.3 60.7 + - - +
102C VAL* 3.4 15.1 + - + -
103C LEU* 2.9 36.4 + - + +
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Residues in contact with SER 100 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12C ASP* 4.3 14.0 + - - -
13C LEU* 3.8 27.5 - - - +
18C PRO* 5.0 2.1 - - - +
98C THR* 2.8 12.9 + - - -
99C ILE* 1.3 81.5 - - - +
101C LYS* 1.3 63.8 + - - +
103C LEU* 3.0 7.8 + - - +
104C LEU* 2.9 44.3 + - - +
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Residues in contact with LYS 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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1129B GLY 4.6 13.6 + - - -
1130B PHE* 6.1 0.7 - - - +
1131B THR* 4.3 25.6 - - - +
88C ILE* 4.4 7.9 - - + -
96C ALA 5.5 0.7 - - - -
97C LEU* 4.1 28.0 - - + +
98C THR* 3.0 28.7 + - + +
100C SER* 1.3 78.0 - - - +
102C VAL* 1.3 56.3 + - - +
104C LEU* 3.6 13.5 + - + +
105C SER* 2.9 30.3 + - - -
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Residues in contact with VAL 102 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65C PRO* 4.8 3.8 - - + -
67C VAL* 4.6 8.3 - - + -
86C LEU* 5.3 1.1 - - + -
88C ILE* 3.7 25.3 - - + +
89C LEU* 3.6 32.3 - - + -
93C TRP* 3.9 21.1 - - + -
98C THR 3.3 14.6 + - - +
99C ILE* 3.4 17.9 - - + +
100C SER 3.2 0.2 - - - -
101C LYS* 1.3 75.6 - - - +
103C LEU* 1.3 63.9 + - + +
105C SER* 3.0 4.0 + - - -
106C ILE* 2.9 41.0 + - + +
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Residues in contact with LEU 103 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13C LEU* 4.5 15.3 - - + -
21C CYS* 4.1 25.8 - - + +
22C SER* 4.1 2.7 - - - +
23C ALA* 3.7 32.1 - - + +
35C ALA* 4.4 9.4 - - + -
37C ILE* 5.2 2.9 - - + +
52C LEU* 4.9 4.3 - - + -
54C ILE* 4.3 12.8 - - + -
67C VAL* 5.6 0.7 - - + -
99C ILE* 2.9 32.9 + - + +
100C SER* 3.0 10.1 + - - +
102C VAL* 1.3 76.7 - - + +
104C LEU* 1.3 60.4 + - + +
106C ILE* 3.1 18.4 + - + +
107C CYS* 2.9 30.1 + - - -
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Residues in contact with LEU 104 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18C PRO* 5.3 11.0 - - + -
21C CYS* 4.7 5.8 - - - -
100C SER* 2.9 44.0 + - - +
101C LYS* 4.1 11.2 - - + +
103C LEU* 1.3 70.9 - - + +
105C SER* 1.3 61.4 + - - +
106C ILE 3.3 0.2 - - - -
107C CYS* 3.8 13.6 - - + +
108C SER* 2.9 29.3 + - - -
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Residues in contact with SER 105 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86C LEU* 4.0 20.2 - - - +
88C ILE* 4.1 16.6 - - - +
101C LYS 2.9 20.9 + - - -
102C VAL* 3.0 13.0 + - - -
104C LEU* 1.3 79.1 - - - +
106C ILE* 1.3 55.4 + - - +
108C SER* 3.5 5.8 + - - -
109C LEU* 2.9 25.8 + - - +
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Residues in contact with ILE 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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37C ILE* 4.2 10.1 - - + -
52C LEU* 3.7 16.4 - - + -
67C VAL* 4.1 9.6 - - + -
69C PHE* 3.7 33.0 - - + -
78C ILE* 5.6 0.4 - - + -
84C ILE* 3.6 26.5 - - + -
86C LEU* 3.7 17.7 - - + -
89C LEU* 5.0 1.1 - - + -
102C VAL* 2.9 26.5 + - + +
103C LEU* 3.5 9.9 - - + +
105C SER* 1.3 72.6 - - - +
107C CYS* 1.3 61.0 + - - +
108C SER 3.1 1.3 - - - -
109C LEU* 2.8 26.3 + - + +
110C LEU* 3.0 15.9 + - + +
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Residues in contact with CYS 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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20C GLN* 5.0 12.2 - - - +
21C CYS* 2.0 55.6 - - - -
37C ILE* 4.3 14.1 - - - -
38C MET 5.9 0.9 - - - -
40C PRO* 4.5 3.1 - - - +
103C LEU 2.9 16.9 + - - +
104C LEU* 3.9 7.6 - - + +
105C SER 3.5 0.2 - - - -
106C ILE* 1.3 74.9 - - - +
108C SER* 1.3 61.6 + - - +
110C LEU* 3.4 22.1 + - - +
111C CYS* 3.7 13.2 + - - -
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Residues in contact with SER 108 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104C LEU 2.9 20.9 + - - -
105C SER* 3.6 7.0 - - - -
107C CYS* 1.3 73.2 - - - +
109C LEU* 1.3 65.0 + - - +
110C LEU 3.1 2.2 + - - -
111C CYS* 3.4 7.1 + - - +
112C ASP* 3.1 27.7 + - - +
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Residues in contact with LEU 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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75C HIS* 2.9 29.1 + - + -
77C ASN* 3.7 38.6 - - + +
78C ILE* 5.1 5.4 - - + -
84C ILE* 4.2 13.7 - - + -
86C LEU* 3.8 31.6 - - + +
105C SER 2.9 15.5 + - - +
106C ILE* 2.8 14.7 + - + +
108C SER* 1.3 77.1 - - - +
110C LEU* 1.3 60.8 + - + +
112C ASP 3.5 20.9 - - - +
113C PRO* 4.2 1.1 - - + -
114C ASN* 4.3 11.2 - - + +
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Residues in contact with LEU 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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37C ILE* 3.9 26.5 - - + -
38C MET 5.0 1.1 - - - +
40C PRO* 4.1 25.6 - - + -
43C SER* 4.7 1.5 + - - -
44C PRO* 5.9 0.2 - - - +
45C TYR* 3.9 28.1 - - + -
50C PHE* 4.8 10.1 - - + -
69C PHE* 4.7 4.0 - - + -
73C ILE* 3.8 30.3 - - + -
75C HIS* 4.0 16.8 + - + -
78C ILE* 4.3 11.0 - - + -
106C ILE* 3.0 16.4 + - + +
107C CYS* 3.6 10.1 - - - +
108C SER 3.1 0.6 - - - -
109C LEU* 1.3 80.5 - - + +
111C CYS* 1.3 65.4 + - - +
112C ASP 3.4 0.3 + - - -
113C PRO* 4.0 7.1 - - - +
134C TYR* 5.4 0.2 + - - -
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Residues in contact with CYS 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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20C GLN* 5.3 0.9 - - - -
40C PRO* 3.6 34.3 - - - -
41C ASN 5.5 1.6 - - - -
42C ASP 6.1 0.7 - - - +
43C SER* 4.2 9.9 - - - +
107C CYS 3.8 9.4 - - - -
108C SER* 3.4 6.5 + - - +
110C LEU* 1.3 74.8 - - - +
112C ASP* 1.3 63.0 + - + +
113C PRO* 3.6 6.3 - - - +
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Residues in contact with ASP 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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108C SER* 3.1 18.3 + - - +
109C LEU* 3.5 14.6 - - - +
111C CYS* 1.3 81.6 - - + +
113C PRO* 1.3 77.5 - - - +
127C TYR* 5.9 0.4 - - - -
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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