Contacts of the helix formed by residues 108 - 120 (chain C) in PDB entry 2GJD
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 108 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8C ARG* 5.0 0.2 - - - +
12C GLU* 3.7 13.7 - - - +
15C LYS* 4.0 29.9 + - - +
106C ALA 3.5 13.2 - - - +
107C ILE* 1.3 80.9 - - - +
109C LEU* 1.3 63.7 + - - +
110C LYS* 3.5 10.6 + - - +
111C GLN* 2.8 45.1 + - - +
112C ILE* 3.1 13.2 + - - +
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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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12C GLU* 2.9 21.9 + - + +
16C TRP* 4.0 20.9 - - + -
26C ALA* 3.7 19.5 - - + -
41C TRP* 3.5 36.3 - - + -
43C ALA* 5.7 0.4 - - + -
62C VAL* 4.4 19.1 - - + -
64C TYR* 3.9 20.6 - - - +
68C TYR* 5.8 0.2 + - - -
108C THR* 1.3 71.9 - - - +
110C LYS* 1.3 58.9 + - - +
112C ILE* 3.0 20.7 + - + +
113C VAL* 2.8 43.5 + - + +
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Residues in contact with LYS 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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15C LYS* 4.6 15.8 - - - +
16C TRP* 4.1 10.2 - - + -
19C ASP* 3.8 32.9 + - - +
20C HIS* 5.7 0.4 - - - -
21C PRO* 3.7 31.2 - - + -
108C THR* 3.2 9.8 + - - +
109C LEU* 1.3 78.2 - - - +
111C GLN* 1.3 66.7 + - + +
113C VAL* 3.4 8.5 - - - +
114C LEU* 3.0 39.1 + - + +
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Residues in contact with GLN 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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96C ILE* 4.0 8.1 - - + +
104C ARG* 4.3 16.8 - - - +
106C ALA 4.0 1.6 - - - +
107C ILE* 3.3 19.1 - - + +
108C THR* 2.8 44.6 + - - +
110C LYS* 1.3 79.6 - - + +
112C ILE* 1.3 62.5 + - - +
114C LEU* 3.9 7.2 - - + +
115C GLY* 3.0 19.4 + - - -
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Residues in contact with ILE 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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60C ILE* 5.7 1.1 - - + -
62C VAL* 5.5 0.9 - - + -
64C TYR* 5.4 3.8 - - + +
68C TYR* 6.1 0.9 - - + +
73C PRO* 3.8 27.6 - - + -
75C VAL* 4.2 24.0 - - + -
94C LEU* 4.4 1.2 - - - +
96C ILE* 3.9 9.9 - - + -
97C LEU* 4.2 17.5 - - + -
103C TRP* 4.3 11.7 - - + -
107C ILE* 3.8 13.5 - - + +
108C THR 3.1 17.2 + - - +
109C LEU* 3.0 28.4 + - + +
111C GLN* 1.3 76.1 - - - +
113C VAL* 1.3 61.1 + - + +
115C GLY* 3.0 3.8 + - - -
116C VAL* 2.9 35.7 + - + +
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Residues in contact with VAL 113 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16C TRP* 3.8 22.2 - - + -
21C PRO* 4.3 5.6 - - + -
24C PHE* 3.5 24.5 - - + -
43C ALA* 4.9 6.7 - - + -
45C ILE* 3.5 26.6 - - + +
60C ILE* 4.5 11.7 - - + -
109C LEU* 2.8 41.2 + - + +
110C LYS* 3.4 11.2 - - - +
112C ILE* 1.3 74.0 - - + +
114C LEU* 1.3 58.0 + - - +
116C VAL* 3.3 5.0 + - - +
117C GLN* 2.8 28.8 + - - +
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Residues in contact with LEU 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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21C PRO* 4.1 17.7 - - + -
24C PHE* 3.8 14.4 - - + -
110C LYS* 3.0 42.8 + - + +
111C GLN* 4.0 6.3 - - + +
113C VAL* 1.3 74.4 - - - +
115C GLY* 1.3 59.4 + - - +
117C GLN* 3.4 24.3 + - - +
118C ASP* 2.8 29.8 + - - +
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Residues in contact with GLY 115 (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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94C LEU* 3.8 20.1 - - - +
96C ILE* 4.9 4.3 - - - -
111C GLN 3.0 11.9 + - - -
112C ILE 3.0 8.6 + - - -
114C LEU* 1.3 74.8 - - - +
116C VAL* 1.3 62.8 + - - +
118C ASP* 3.4 7.4 + - - +
119C LEU* 3.1 22.9 + - - +
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Residues in contact with VAL 116 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45C ILE* 4.2 17.3 - - + -
60C ILE* 4.9 3.6 - - + -
75C VAL* 4.5 10.8 - - + -
77C PHE* 3.6 32.5 - - + -
92C ILE* 3.9 26.2 - - + -
94C LEU* 4.0 15.5 - - + -
97C LEU* 5.2 1.3 - - + -
112C ILE* 2.9 22.8 + - + +
113C VAL* 3.7 9.0 - - - +
115C GLY* 1.3 73.8 - - - +
117C GLN* 1.3 65.7 + - - +
119C LEU* 3.1 18.3 + - + +
120C LEU* 3.4 11.9 + - + +
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Residues in contact with GLN 117 (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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24C PHE* 3.4 29.1 - - + -
45C ILE* 3.7 14.1 - - + +
46C PRO* 2.9 32.4 + - - +
47C GLY 4.3 1.6 + - - -
48C LYS* 3.8 42.4 - - + +
113C VAL 2.8 21.5 + - - +
114C LEU* 3.6 17.0 - - - +
116C VAL* 1.3 73.1 - - - +
118C ASP* 1.3 61.7 + - - +
120C LEU* 3.2 23.5 + - + +
121C ASP* 4.4 1.0 + - - +
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Residues in contact with ASP 118 (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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48C LYS* 3.8 25.2 + - - +
114C LEU 2.8 20.8 + - - +
115C GLY* 3.7 8.1 - - - +
116C VAL 3.3 0.4 - - - -
117C GLN* 1.3 73.6 - - - +
119C LEU* 1.3 63.6 + - - +
120C LEU 3.3 0.5 + - - -
121C ASP* 3.8 2.9 + - - +
122C SER* 3.7 25.4 + - - +
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Residues in contact with LEU 119 (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 PHE* 6.3 0.4 - - + -
83C HIS* 2.9 18.2 + - + +
85C ASN* 3.1 36.6 - - + +
86C VAL* 5.7 0.7 - - + -
92C ILE* 3.8 19.1 - - + -
93C CYS 3.5 23.3 - - - +
94C LEU* 4.0 15.9 - - + -
115C GLY 3.1 12.5 + - - +
116C VAL* 3.1 12.0 + - + +
118C ASP* 1.3 78.8 + - - +
120C LEU* 1.3 67.6 + - + +
122C SER 3.1 27.2 + - - +
124C ASN* 4.1 13.2 - - + +
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Residues in contact with LEU 120 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45C ILE* 4.1 18.2 - - + -
46C PRO 4.5 0.7 - - - +
47C GLY* 4.3 12.3 - - - -
48C LYS 5.4 0.4 - - - +
53C TRP* 3.2 49.6 + - + -
58C TYR* 3.8 29.4 - - + -
77C PHE* 3.9 29.8 - - + -
81C PHE* 4.7 1.6 - - + -
83C HIS* 3.1 19.7 + - + -
116C VAL* 3.6 7.9 - - + +
117C GLN* 3.2 18.0 + - + +
119C LEU* 1.3 81.0 - - + +
121C ASP* 1.3 60.0 + - + +
123C PRO* 4.4 3.5 - - - +
144C TYR* 4.5 1.4 + - - -
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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