Contacts of the helix formed by residues 98 - 119 (chain C) in PDB entry 3V9G
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 ASP 98 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75C THR* 4.2 17.1 - - - +
96C TYR 3.6 2.5 + - - +
97C ALA* 1.3 75.4 - - - +
99C LYS* 1.3 68.9 + - - +
100C SER* 3.1 12.9 + - - +
101C LEU* 2.9 36.9 + - - +
102C LEU* 3.0 22.3 + - - +
268C LEU* 4.2 6.5 - - - -
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Residues in contact with LYS 99 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98C ASP* 1.3 73.2 - - - +
100C SER* 1.3 64.5 + - - +
102C LEU* 3.4 3.4 + - - +
103C ASN* 3.0 36.6 + - - +
268C LEU* 4.0 15.2 - - + +
272C THR* 4.4 19.5 - - + +
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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
----------------------------------------------------------
98C ASP* 3.1 12.4 - - - +
99C LYS* 1.3 79.9 - - - +
101C LEU* 1.3 63.7 + - - +
103C ASN* 3.4 5.2 + - - +
104C LYS* 3.0 22.5 + - - +
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Residues in contact with LEU 101 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66C CYS* 4.0 18.2 - - + -
68C VAL* 3.6 25.6 - - + -
73C VAL* 3.8 34.1 - - + -
75C THR* 4.0 11.0 - - + -
97C ALA* 3.7 26.0 - - + -
98C ASP* 2.9 24.5 + - - +
100C SER* 1.3 71.4 + - - +
102C LEU* 1.3 62.1 + - - +
104C LYS* 3.2 11.4 + - + +
105C ALA* 2.9 27.6 + - - +
262C VAL* 5.0 2.0 - - + -
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Residues in contact with LEU 102 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97C ALA* 3.7 22.7 - - + +
98C ASP 3.0 15.0 + - - +
99C LYS 3.7 4.0 - - - +
101C LEU* 1.3 74.5 - - - +
103C ASN* 1.3 59.3 + - - +
105C ALA* 3.3 6.6 + - - +
106C ILE* 3.0 32.7 + - + +
231C LEU* 3.8 7.8 - - + +
262C VAL* 3.9 19.5 - - + +
264C ALA* 4.7 1.8 - - + -
268C LEU* 3.6 31.9 - - + -
269C PHE* 3.9 36.1 - - + -
272C THR* 3.8 25.1 - - + +
273C VAL* 5.8 0.9 - - + -
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Residues in contact with ASN 103 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99C LYS* 3.0 25.7 + - - +
100C SER* 3.9 4.8 - - - +
102C LEU* 1.3 75.1 - - - +
104C LYS* 1.3 63.8 + - - +
106C ILE* 3.6 22.8 - - - +
107C GLU* 2.9 26.0 + - - +
272C THR* 3.8 18.0 + - - +
276C SER* 5.3 3.6 - - - +
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Residues in contact with LYS 104 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68C VAL* 4.5 5.8 - - + +
100C SER* 3.0 14.4 + - - +
101C LEU* 3.2 17.9 + - + +
103C ASN* 1.3 75.6 - - - +
105C ALA* 1.3 57.2 + - - +
107C GLU* 3.5 5.7 + - - +
108C ALA* 3.0 30.8 + - - +
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Residues in contact with ALA 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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68C VAL* 3.7 25.3 - - + +
101C LEU 2.9 13.6 + - - +
102C LEU* 3.3 12.8 - - - +
104C LYS* 1.3 75.1 - - - +
106C ILE* 1.3 60.1 + - - +
108C ALA 3.5 0.2 + - - -
109C ALA* 2.9 27.4 + - - +
231C LEU* 4.0 11.4 - - + -
260C GLN* 3.2 28.2 + - + +
262C VAL* 4.4 4.5 - - + -
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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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102C LEU 3.0 18.3 + - - +
103C ASN* 3.6 29.2 - - - +
105C ALA* 1.3 72.8 - - - +
107C GLU* 1.3 66.5 + - - +
109C ALA* 3.3 2.9 + - - +
110C LEU* 3.0 42.1 + - + +
203C PHE* 3.6 45.5 - - + -
231C LEU* 3.7 22.7 - - + -
272C THR* 4.8 7.9 - - + +
273C VAL* 4.9 2.5 - - + -
276C SER* 3.9 16.2 - - - +
278C HIS* 4.7 3.1 - - + -
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Residues in contact with GLU 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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103C ASN 2.9 16.9 + - - +
104C LYS* 3.8 6.5 - - - +
106C ILE* 1.3 78.0 - - - +
108C ALA* 1.3 62.4 + - - +
110C LEU* 3.5 8.7 + - - +
111C ALA* 3.2 22.5 + - - +
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Residues in contact with ALA 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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68C VAL* 4.6 5.4 - - + -
104C LYS 3.0 19.0 + - - +
105C ALA 4.5 0.2 - - - -
107C GLU* 1.3 74.7 - - - +
109C ALA* 1.3 67.5 + - - +
111C ALA* 3.4 7.3 + - - +
112C ALA* 3.3 15.9 + - - +
257C ASN* 3.3 34.5 + - - +
260C GLN* 3.9 5.2 - - - +
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Residues in contact with ALA 109 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105C ALA 2.9 19.5 + - - +
106C ILE* 3.6 5.6 - - - +
108C ALA* 1.3 75.0 - - - +
110C LEU* 1.3 63.3 + - - +
112C ALA* 3.0 12.0 + - - -
113C ARG 3.2 9.5 + - - -
203C PHE* 4.9 2.7 - - + -
229C VAL* 3.3 33.4 - - + +
230C VAL 5.0 0.4 - - - +
231C LEU* 4.5 7.0 - - + -
257C ASN 3.3 19.1 - - - +
260C GLN* 3.7 10.9 - - + +
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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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106C ILE* 3.0 28.9 + - + +
107C GLU* 3.7 7.4 - - - +
108C ALA 3.3 0.2 - - - -
109C ALA* 1.3 76.8 - - - +
111C ALA* 1.3 61.0 + - - +
112C ALA 3.5 0.5 + - - -
113C ARG* 3.5 21.6 + - - +
114C LYS 4.7 1.9 + - - -
202C GLY* 3.6 39.7 - - - +
203C PHE* 3.9 8.1 - - + +
229C VAL* 4.7 1.1 - - + -
278C HIS* 3.3 48.0 - - + +
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Residues in contact with ALA 111 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107C GLU 3.2 16.5 + - - +
108C ALA* 3.9 7.2 - - - +
109C ALA 3.2 0.2 - - - -
110C LEU* 1.3 78.4 - - - +
112C ALA* 1.3 59.0 + - - +
113C ARG 3.4 0.4 + - - -
114C LYS* 5.1 2.0 + - - +
115C GLU* 5.8 0.5 + - - +
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Residues in contact with ALA 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 ALA 3.3 3.7 + - - +
109C ALA 3.0 8.7 + - - +
111C ALA* 1.3 78.9 - - - +
113C ARG* 1.3 62.0 + - - +
114C LYS 3.6 1.5 + - - -
115C GLU* 3.7 7.9 + - - +
116C TRP* 3.4 20.6 + - - +
229C VAL* 4.5 1.3 - - - -
256C PRO 4.1 7.4 - - - +
257C ASN* 3.7 29.6 - - + +
258C ILE* 4.1 10.4 - - + +
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Residues in contact with ARG 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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109C ALA 3.2 4.8 + - - +
110C LEU* 3.5 17.7 + - - +
111C ALA 3.4 2.0 - - - -
112C ALA* 1.3 75.6 - - - +
114C LYS* 1.3 69.7 + - - +
116C TRP* 3.0 3.2 + - - +
117C ASP* 2.7 59.4 + - - +
199C GLY 4.6 2.6 + - - -
200C LEU 3.8 17.9 + - - -
201C GLU* 3.6 29.7 + - - +
202C GLY* 3.1 33.7 - - - +
227C GLY 4.2 12.5 + - - +
229C VAL* 3.6 28.3 - - + +
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Residues in contact with LYS 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 LEU 4.7 2.0 + - - -
111C ALA 5.1 1.8 + - - +
112C ALA 3.6 0.6 - - - -
113C ARG* 1.3 89.3 - - - +
115C GLU* 1.3 57.3 + - - +
117C ASP* 3.4 6.3 + - - +
118C LEU* 2.9 41.6 + - + +
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Residues in contact with GLU 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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111C ALA 5.8 0.2 + - - -
112C ALA* 3.7 7.7 + - - +
113C ARG 3.3 0.4 - - - -
114C LYS* 1.3 77.5 - - - +
116C TRP* 1.3 57.1 + - - +
118C LEU* 3.4 8.9 + - - +
119C LYS* 3.0 27.2 + - - +
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Residues in contact with TRP 116 (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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112C ALA 3.4 5.1 + - - +
113C ARG 3.0 6.9 + - - +
115C GLU* 1.3 77.4 - - - +
117C ASP* 1.3 64.8 + - - +
119C LYS* 3.2 17.9 + - + +
124C ARG* 3.1 47.7 + - + -
127C ILE* 3.9 16.4 - - + -
128C PHE* 4.7 4.7 - + - -
224C ALA 2.9 32.2 + - - -
227C GLY* 3.5 20.5 - - - -
228C ASN 3.2 22.2 + - - -
229C VAL* 4.6 2.0 - - + -
254C LEU* 3.9 18.4 - - + -
255C PRO* 3.6 33.2 - - + -
258C ILE* 3.5 38.9 - - + +
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Residues in contact with ASP 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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113C ARG* 2.7 38.9 + - - +
114C LYS* 3.8 5.5 - - - +
116C TRP* 1.3 73.4 - - - +
118C LEU* 1.3 60.6 + - - +
119C LYS 3.7 0.7 - - - +
124C ARG* 3.1 20.0 + - - +
197C TYR 4.5 2.3 - - - +
198C ARG* 3.8 15.7 - - - +
199C GLY* 3.1 28.3 + - - +
226C MET 4.8 0.2 - - - +
227C GLY* 3.7 16.0 - - - +
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Residues in contact with LEU 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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114C LYS* 2.9 29.0 + - + +
115C GLU* 3.8 7.4 - - - +
116C TRP 3.1 0.2 - - - -
117C ASP* 1.3 78.5 - - + +
119C LYS* 1.3 63.8 + - - +
120C PRO* 3.3 7.1 - - - +
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Residues in contact with LYS 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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115C GLU 3.0 13.5 + - - +
116C TRP* 3.2 19.0 + - + +
117C ASP 3.7 0.7 - - - +
118C LEU* 1.3 76.4 - - - +
120C PRO* 1.3 72.5 - - + +
123C ASP* 4.9 6.5 - - + +
124C ARG* 2.8 38.7 + - + -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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