Contacts of the helix formed by residues 104 - 122 (chain C) in PDB entry 4IRQ
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 ARG 104 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101C PHE* 3.5 21.9 - - + -
102C ARG 3.4 4.8 + - - -
103C GLU* 1.3 91.9 + - - +
105C PHE* 1.3 57.9 - - - +
107C GLU* 3.2 21.3 + - - +
108C LEU 3.0 23.6 + - - -
164C VAL* 3.8 18.6 - - + -
165C ASP* 6.4 0.9 - - - -
259C HIS* 5.4 2.2 + - - -
264C ARG* 3.6 49.5 + - - +
265C LYS 4.4 13.1 + - - -
402C UDP 3.1 70.4 + - + +
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Residues in contact with PHE 105 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101C PHE* 3.9 8.7 - + + -
103C GLU* 3.6 14.3 + - - +
104C ARG* 1.3 75.3 - - - +
106C GLU* 1.3 79.0 + - - +
108C LEU* 3.2 13.7 + - + +
109C LEU* 3.1 60.0 + - + +
264C ARG* 4.2 3.0 - - - +
300C LEU* 6.0 4.0 - - + -
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Residues in contact with GLU 106 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104C ARG 3.4 0.2 - - - -
105C PHE* 1.3 90.1 + - + +
107C GLU* 1.3 69.7 + - - +
109C LEU* 3.3 21.5 + - + +
110C VAL* 3.5 16.2 + - - +
263C TRP* 5.4 2.4 + - - -
264C ARG* 2.8 26.7 + - - +
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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
----------------------------------------------------------
104C ARG* 3.2 21.2 + - + +
106C GLU* 1.3 77.7 - - + +
108C LEU* 1.3 50.2 + - - +
110C VAL* 3.0 6.3 + - - +
111C PHE* 2.7 36.4 + - - +
164C VAL* 3.8 22.4 - - + +
165C ASP* 4.0 11.0 - - + +
258C LEU* 3.5 41.7 - - + +
260C ASP 5.7 0.2 + - - -
264C ARG* 3.0 50.6 + - - +
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Residues in contact with LEU 108 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99C VAL* 5.4 0.9 - - + -
101C PHE* 3.9 25.1 - - + -
104C ARG 3.0 13.6 + - - +
105C PHE* 3.5 20.2 - - + +
107C GLU* 1.3 76.4 - - - +
109C LEU* 1.3 63.9 + - + +
111C PHE* 3.1 13.9 + - + -
112C VAL* 3.1 40.5 + - + +
130C VAL* 3.9 26.2 - - + -
164C VAL* 3.9 21.4 - - + +
300C LEU* 4.2 25.1 - - + -
302C VAL* 4.5 4.2 - - + +
309C VAL* 5.4 0.9 - - + -
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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
----------------------------------------------------------
105C PHE* 3.1 63.4 + - + +
106C GLU* 3.5 13.5 - - + +
107C GLU 3.3 0.2 - - - -
108C LEU* 1.3 76.9 - - + +
110C VAL* 1.3 59.8 + - + +
113C PRO* 3.2 21.5 - - - +
302C VAL* 3.3 32.6 - - + +
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Residues in contact with VAL 110 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106C GLU 3.7 12.6 - - - +
107C GLU* 3.0 7.0 + - - +
109C LEU* 1.3 78.9 - - + +
111C PHE* 1.3 66.4 + - - +
113C PRO* 3.4 3.7 - - - +
114C HIS* 3.2 22.3 + - + +
167C LEU* 3.7 26.7 - - + -
258C LEU* 4.0 15.5 - - + -
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Residues in contact with PHE 111 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97C VAL* 4.5 3.6 - - + -
99C VAL* 3.7 28.5 - - + -
107C GLU 2.7 15.6 + - - +
108C LEU* 3.1 10.3 + - + +
110C VAL* 1.3 75.3 - - - +
112C VAL* 1.3 73.8 + - + +
114C HIS* 3.3 2.3 + - - +
115C MET* 2.8 58.0 + - + +
128C ILE* 4.3 10.5 - - + -
162C HIS* 3.5 26.7 - + - -
163C ASP 3.4 19.3 - - - -
164C VAL* 3.3 29.6 - - + +
166C LEU 4.4 2.0 - - - -
167C LEU* 3.7 20.4 - - + +
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Residues in contact with VAL 112 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108C LEU* 3.1 36.0 + - + +
111C PHE* 1.3 83.0 - - + +
113C PRO* 1.4 63.6 - - + +
115C MET* 3.4 1.7 + - - +
116C ARG* 3.0 27.4 + - - +
128C ILE* 4.0 13.2 - - + +
130C VAL* 5.1 0.2 - - + -
302C VAL* 4.1 10.1 - - + -
305C ALA* 3.5 30.1 - - + +
306C PRO 3.8 14.4 - - - +
307C CYS* 4.1 22.2 - - + -
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Residues in contact with PRO 113 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109C LEU 3.2 25.6 - - - +
110C VAL* 3.4 7.9 - - - +
112C VAL* 1.4 90.3 - - + +
114C HIS* 1.3 64.6 + - - +
116C ARG* 3.2 2.7 + - + +
117C ARG* 2.9 26.1 + - - +
302C VAL* 3.4 25.8 - - + +
303C GLY* 5.1 5.6 - - - +
305C ALA* 3.7 12.3 - - + -
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Residues in contact with HIS 114 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110C VAL* 3.2 22.8 + - + +
111C PHE* 3.5 4.9 - - - +
113C PRO* 1.3 79.6 - - - +
115C MET* 1.3 75.1 + - - +
117C ARG* 3.3 12.6 + - - +
118C PHE* 2.9 34.8 + + + +
167C LEU* 3.6 37.3 - - + +
168C PRO* 2.8 31.3 + - + +
169C LEU* 3.9 13.7 - - + -
256C ARG* 5.3 3.0 + - - -
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Residues in contact with MET 115 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97C VAL* 5.4 3.6 - - + -
111C PHE* 2.8 55.5 + - + +
112C VAL 3.9 2.9 - - - +
114C HIS* 1.3 76.0 - - + +
116C ARG* 1.3 62.0 + - - +
118C PHE* 4.2 4.5 - - + -
119C LEU* 2.9 58.5 + - + +
128C ILE* 4.0 15.0 - - + -
162C HIS* 3.7 22.0 - - + +
168C PRO* 3.7 32.8 - - + -
175C TYR* 4.0 17.5 - - + -
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Residues in contact with ARG 116 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85C GLU* 3.2 50.8 + - - +
112C VAL 3.0 18.0 + - - +
113C PRO* 3.6 4.3 - - + +
115C MET* 1.3 75.6 - - - +
117C ARG* 1.3 64.1 + - - +
120C SER* 2.8 37.4 + - - +
126C HIS* 3.9 15.7 + - - +
128C ILE* 4.5 4.4 - - + +
304C GLY 4.5 5.1 + - - -
305C ALA* 3.5 28.7 - - + +
306C PRO* 3.6 24.8 - - + +
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Residues in contact with ARG 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 PRO 2.9 17.5 + - - +
114C HIS* 3.4 13.0 + - - +
116C ARG* 1.3 80.3 - - - +
118C PHE* 1.3 68.6 + - - +
120C SER* 3.9 2.9 - - - -
121C ARG* 3.0 70.5 + - + +
171C GLU* 4.4 6.5 + - - -
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Residues in contact with PHE 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 HIS* 2.9 27.4 + - + +
115C MET* 3.8 9.9 - - + +
117C ARG* 1.3 81.3 - - - +
119C LEU* 1.3 73.9 + - + +
121C ARG* 3.6 6.5 + - - +
122C LYS* 3.2 46.3 + - + +
168C PRO* 3.6 43.1 - - + -
169C LEU 5.5 0.4 - - - -
170C ASN 3.7 22.4 - - - -
171C GLU* 3.9 24.8 - - + -
173C LEU* 4.7 1.1 - - + -
175C TYR* 3.5 33.4 - + - -
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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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95C LEU* 4.1 9.9 - - + -
97C VAL* 3.8 21.3 - - + -
115C MET* 2.9 34.8 + - + +
118C PHE* 1.3 86.2 - - + +
120C SER* 1.3 58.6 + - - +
122C LYS* 3.3 3.6 + - - -
123C LYS 3.1 7.1 + - - -
124C ILE* 2.9 47.1 + - + +
126C HIS* 3.3 42.8 - - + +
128C ILE* 5.3 0.7 - - + -
175C TYR* 3.8 28.3 - - + -
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Residues in contact with SER 120 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85C GLU* 3.9 18.1 + - - +
90C TRP* 3.6 24.8 - - - -
116C ARG* 2.8 27.7 + - - +
117C ARG* 3.9 3.4 - - - -
119C LEU* 1.3 75.1 - - - +
121C ARG* 1.3 65.6 + - - +
123C LYS* 3.0 15.6 + - - +
126C HIS* 3.6 13.0 - - - -
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Residues in contact with ARG 121 (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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117C ARG* 3.0 59.3 + - + +
118C PHE* 3.9 4.9 - - - +
120C SER* 1.3 76.8 - - - +
122C LYS* 1.3 58.2 + - - +
123C LYS* 3.3 15.1 + - - +
171C GLU* 2.8 44.2 + - - +
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Residues in contact with LYS 122 (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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118C PHE* 3.2 51.7 + - + +
119C LEU 3.3 4.2 + - - +
120C SER 3.2 0.8 - - - -
121C ARG* 1.3 74.4 - - - +
123C LYS* 1.3 69.6 + - - +
124C ILE* 3.3 28.8 + - + +
171C GLU* 2.6 42.0 + - + +
172C GLU 4.4 0.6 - - - -
173C LEU 2.6 24.2 + - - -
174C ASP* 4.7 1.0 - - - +
175C TYR 4.2 4.9 - - - +
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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