Contacts of the helix formed by residues 104 - 122 (chain A) in PDB entry 4IRP
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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101A PHE* 3.3 25.2 - - + -
102A ARG 3.4 2.7 + - - +
103A GLU* 1.3 85.1 + - - +
105A PHE* 1.3 64.0 + - - +
106A GLU 3.3 2.9 - - - -
107A GLU* 3.3 32.8 + - - +
108A LEU 2.9 17.8 + - - -
164A VAL* 3.7 17.7 - - + +
165A ASP* 4.1 13.5 + - - -
259A HIS* 5.5 6.0 + - - -
401A UDP 2.9 81.7 + - - +
103B GLU* 4.3 0.9 - - - -
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Residues in contact with PHE 105 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101A PHE* 3.7 7.5 - - - -
104A ARG* 1.3 76.0 - - - +
106A GLU* 1.3 63.1 + - - +
108A LEU* 3.1 16.1 + - + +
109A LEU* 3.2 42.7 + - + +
300A LEU* 6.4 0.2 - - + -
101B PHE* 3.5 30.5 - + + -
103B GLU* 3.4 19.5 + - - +
105B PHE* 3.5 35.0 - + + -
108B LEU* 3.7 30.3 - - + -
130B VAL* 4.7 1.1 - - + -
132B ASN* 4.0 17.3 - - - -
300B LEU* 4.2 5.8 - - + -
309B VAL* 3.9 29.4 - - + -
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Residues in contact with GLU 106 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104A ARG 3.3 0.8 - - - -
105A PHE* 1.3 81.7 - - - +
107A GLU* 1.3 71.1 + - + +
109A LEU* 3.4 21.3 + - - +
110A VAL* 3.7 12.5 + - + +
103B GLU* 4.9 5.1 + - - +
132B ASN* 4.8 5.2 - - - +
134B VAL* 3.6 37.5 - - + +
311B ASN* 4.1 18.5 + - - +
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Residues in contact with GLU 107 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103A GLU 4.8 0.2 - - - +
104A ARG* 3.3 43.5 + - - +
106A GLU* 1.3 82.5 + - - +
108A LEU* 1.3 57.8 + - - +
110A VAL* 3.1 5.9 + - - +
111A PHE* 2.8 29.8 + - - +
164A VAL* 4.0 15.5 - - + +
165A ASP* 4.0 10.7 - - + +
258A LEU* 3.8 38.6 - - + +
259A HIS* 4.0 20.3 + - - +
103B GLU* 5.1 2.1 - - - +
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Residues in contact with LEU 108 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99A VAL* 5.3 1.6 - - + -
101A PHE* 3.8 13.7 - - + -
104A ARG 2.9 14.5 + - - +
105A PHE* 3.1 12.5 + - + +
107A GLU* 1.3 75.0 - - - +
109A LEU* 1.3 60.1 + - + +
111A PHE* 4.0 5.6 - - + -
112A VAL* 3.0 52.1 + - + +
128A ILE* 5.8 0.2 - - + -
130A VAL* 3.5 33.0 - - + -
164A VAL* 3.9 18.8 - - + +
300A LEU* 4.0 15.7 - - + -
302A VAL* 5.5 2.5 - - + -
105B PHE* 3.8 35.7 - - + -
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Residues in contact with LEU 109 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105A PHE* 3.2 42.1 + - + +
106A GLU* 3.6 8.7 - - - +
107A GLU 3.2 0.4 - - - -
108A LEU* 1.3 82.9 - - + +
110A VAL* 1.3 59.7 + - + +
113A PRO* 3.2 21.1 - - - +
302A VAL* 3.4 19.2 - - + +
132B ASN* 4.4 1.1 - - - +
298B THR* 4.3 20.5 - - + +
300B LEU* 4.1 25.8 - - + -
309B VAL* 3.9 27.6 - - + -
311B ASN* 4.0 20.4 - - - +
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Residues in contact with VAL 110 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106A GLU* 3.7 13.2 + - + +
107A GLU* 3.1 8.1 + - - +
109A LEU* 1.3 78.2 - - + +
111A PHE* 1.3 68.0 + - - +
112A VAL 3.5 0.2 - - - -
113A PRO* 3.6 3.7 - - - +
114A HIS* 3.0 28.2 + - + +
167A LEU* 3.7 27.8 - - + -
256A ARG* 4.2 19.3 - - - +
258A LEU* 4.4 10.3 - - + -
311B ASN* 6.2 2.0 - - - +
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Residues in contact with PHE 111 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97A VAL* 4.2 4.0 - - + -
99A VAL* 3.4 32.5 - - + -
107A GLU 2.8 17.2 + - - +
108A LEU* 3.1 6.5 + - + +
110A VAL* 1.3 78.6 - - - +
112A VAL* 1.3 69.3 + - + +
114A HIS* 3.6 0.2 - - - +
115A MET* 2.9 56.9 + - + +
128A ILE* 4.4 11.7 - - + -
162A HIS* 3.5 30.1 - + - -
163A ASP 3.3 19.5 - - - -
164A VAL* 3.2 36.1 - - + +
166A LEU 4.4 1.1 - - - -
167A LEU* 3.6 20.9 - - + -
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Residues in contact with VAL 112 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108A LEU* 3.0 42.2 + - + +
111A PHE* 1.3 81.2 - - + +
113A PRO* 1.3 71.1 - - + +
115A MET 3.6 0.2 + - - -
116A ARG* 3.1 21.9 + - + +
128A ILE* 4.0 13.9 - - + +
302A VAL* 4.1 11.4 - - + -
305A ALA* 3.2 32.5 - - + +
306A PRO 3.9 11.0 - - - +
307A CYS* 4.0 24.2 - - + -
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Residues in contact with PRO 113 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84A TRP* 5.3 0.2 - - + -
109A LEU 3.2 25.1 - - - +
110A VAL* 3.6 4.9 - - - +
112A VAL* 1.3 92.2 - - + +
114A HIS* 1.3 66.5 + - - +
116A ARG* 3.6 1.2 - - - +
117A ARG* 3.1 50.1 + - - +
302A VAL* 3.7 21.1 - - + +
303A GLY* 5.4 2.9 - - - +
305A ALA* 3.7 17.7 - - + -
298B THR* 6.2 0.2 - - + -
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Residues in contact with HIS 114 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110A VAL* 3.0 26.2 + - + +
111A PHE* 3.3 6.3 + - - +
113A PRO* 1.3 76.7 - - - +
115A MET* 1.3 77.0 + - - +
117A ARG* 3.7 4.6 - - - +
118A PHE* 2.9 32.8 + + + +
167A LEU* 3.8 33.3 - - + +
168A PRO* 2.8 29.7 + - + +
169A LEU* 4.0 14.4 - - + -
256A ARG* 4.9 7.8 + - - -
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Residues in contact with MET 115 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97A VAL* 5.4 3.4 - - + -
111A PHE* 2.9 53.9 + - + +
114A HIS* 1.3 74.8 - - + +
116A ARG* 1.3 60.6 + - - +
118A PHE* 4.3 3.6 - - + -
119A LEU* 2.8 57.7 + - + +
126A HIS* 4.4 2.7 - - - -
128A ILE* 3.9 16.2 - - + -
162A HIS* 3.7 24.2 - - + +
168A PRO* 3.4 34.5 - - + -
175A TYR* 3.8 18.8 - - + -
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Residues in contact with ARG 116 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84A TRP* 3.3 46.6 + - + -
86A GLU* 5.6 2.8 + - - -
90A TRP* 6.3 0.4 - - - -
112A VAL* 3.1 18.7 + - - +
113A PRO 3.6 4.7 - - - +
115A MET* 1.3 76.4 - - - +
117A ARG* 1.3 57.4 + - - +
120A SER* 2.6 46.4 + - - -
126A HIS* 3.2 54.7 + - - +
127A HIS 5.1 0.2 - - - +
128A ILE* 4.7 11.8 - - + +
305A ALA* 3.8 9.0 - - + -
306A PRO* 3.4 43.9 + - - +
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Residues in contact with ARG 117 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81A PRO* 5.0 0.4 - - - +
83A HIS* 4.0 16.6 - - - +
84A TRP* 3.5 33.1 - - + +
113A PRO* 3.1 41.4 + - - +
114A HIS* 3.7 3.8 - - - +
116A ARG* 1.3 77.8 - - - +
118A PHE* 1.3 67.7 + - - +
121A ARG* 2.8 32.2 + - + +
303A GLY 5.2 1.8 + - - -
404A ACT 2.7 40.6 + - - +
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Residues in contact with PHE 118 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114A HIS* 2.9 29.7 + - + +
115A MET* 3.8 6.7 - - + +
117A ARG* 1.3 74.4 - - - +
119A LEU* 1.3 76.8 + - + +
121A ARG* 3.5 3.3 + - - +
122A LYS* 3.3 49.5 + - + +
168A PRO* 3.7 38.4 - - + -
169A LEU 4.7 1.3 - - - -
170A ASN 3.4 36.8 - - - -
171A GLU* 3.8 10.0 - - + +
173A LEU* 4.4 1.8 - - + -
175A TYR* 3.5 31.2 - + - -
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Residues in contact with LEU 119 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95A LEU* 4.0 15.3 - - + -
97A VAL* 4.1 7.4 - - + -
115A MET* 2.8 40.7 + - + +
118A PHE* 1.3 82.2 - - + +
120A SER* 1.3 59.1 + - - +
122A LYS* 3.1 4.7 + - - -
123A LYS 3.0 7.6 + - - -
124A ILE* 2.8 44.4 + - + +
126A HIS* 3.5 41.1 - - + +
175A TYR* 3.7 40.4 - - + -
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Residues in contact with SER 120 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83A HIS* 3.6 22.7 - - - +
84A TRP* 3.8 15.1 + - - -
90A TRP* 3.7 25.8 - - - -
116A ARG* 2.6 40.4 + - - -
117A ARG 3.9 1.6 - - - -
119A LEU* 1.3 76.6 - - - +
121A ARG* 1.3 66.4 + - - +
123A LYS* 3.0 15.9 + - - +
126A HIS* 3.7 5.4 - - - -
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Residues in contact with ARG 121 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83A HIS* 3.5 35.5 - - + +
117A ARG* 2.8 22.2 + - + +
118A PHE* 4.0 3.6 - - - +
120A SER* 1.3 77.6 - - - +
122A LYS* 1.3 56.9 + - - +
123A LYS* 3.1 9.3 + - - +
171A GLU* 3.7 28.4 + - - +
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Residues in contact with LYS 122 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118A PHE* 3.3 48.6 + - + +
119A LEU 3.1 9.1 + - - +
121A ARG* 1.3 76.0 - - - +
123A LYS* 1.3 70.6 + - - +
124A ILE* 3.2 27.1 + - + +
171A GLU* 2.8 42.9 + - + +
172A GLU 4.6 0.8 - - - -
173A LEU 2.8 24.9 + - - -
174A ASP* 4.6 2.4 + - - +
175A TYR 4.4 4.7 - - - +
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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