Contacts of the helix formed by residues 104 - 119 (chain A) in PDB entry 2I91
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 104 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65A ILE* 4.1 13.9 - - + +
68A GLY* 5.4 5.6 - - - +
70A GLY* 4.7 2.6 - - - -
71A CYS* 5.0 0.7 - - - -
102A CYS* 3.1 18.2 - - - +
103A SER* 1.3 84.9 + - - +
105A ILE* 1.3 66.1 + - - +
106A LYS* 3.1 24.6 - - - +
107A THR* 2.8 30.1 + - - +
108A LYS* 3.6 12.8 + - - +
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Residues in contact with ILE 105 (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 SER 4.3 5.2 - - - +
104A ASP* 1.3 76.7 - - - +
106A LYS* 1.3 66.0 + - + +
107A THR 3.3 1.3 - - - -
108A LYS* 3.8 26.5 - - + +
109A GLN* 3.0 34.7 + - - +
537B LEU* 3.1 49.1 - - + -
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Residues in contact with LYS 106 (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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71A CYS* 3.9 21.8 - - - -
104A ASP* 3.1 15.3 - - - +
105A ILE* 1.3 85.1 - - + +
107A THR* 1.3 57.8 + - - +
109A GLN* 3.8 19.6 - - - +
110A ALA* 3.0 28.6 + - - +
113A ARG* 4.8 3.6 + - - +
532B ASN* 3.8 28.3 - - - +
537B LEU* 4.7 24.2 + - + +
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Residues in contact with THR 107 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A ILE* 4.9 0.9 - - + -
70A GLY* 2.8 45.4 - - - +
71A CYS* 3.6 7.6 + - - -
74A VAL* 4.1 2.3 - - + +
99A CYS* 3.8 22.9 - - + -
102A CYS* 3.5 27.4 - - - -
104A ASP* 2.8 20.5 + - - +
106A LYS* 1.3 76.0 - - - +
108A LYS* 1.3 60.1 + - - +
110A ALA* 3.1 5.1 + - - +
111A ALA* 2.8 27.2 + - - +
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Residues in contact with LYS 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 CYS 3.5 10.1 + - - +
100A SER 3.4 32.3 - - - +
101A GLN* 3.7 8.7 + - - +
102A CYS 3.6 22.3 + - - +
103A SER* 4.5 3.8 + - - +
104A ASP 3.6 11.6 + - - +
105A ILE* 3.6 24.3 + - + +
106A LYS 3.4 0.2 - - - -
107A THR* 1.3 78.5 - - - +
109A GLN* 1.3 63.9 + - - +
111A ALA* 3.0 13.7 + - - +
112A PHE* 3.2 28.6 + - + -
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Residues in contact with GLN 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 ILE 3.0 21.2 + - - +
106A LYS* 3.8 17.5 - - - +
108A LYS* 1.3 76.8 - - - +
110A ALA* 1.3 58.0 + - - +
112A PHE* 4.0 6.1 + - - +
113A ARG* 3.1 41.4 + - - +
528B ASP* 2.5 37.8 + - - -
531B ARG* 4.7 8.9 - - - +
532B ASN* 3.5 21.6 + - - +
537B LEU* 5.4 1.2 - - - +
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Residues in contact with ALA 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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71A CYS* 4.2 15.0 - - + -
74A VAL* 3.6 23.9 - - + +
106A LYS 3.0 17.3 + - - +
107A THR* 3.4 7.2 - - - +
108A LYS 3.0 0.2 - - - -
109A GLN* 1.3 76.2 - - - +
111A ALA* 1.3 65.8 + - - +
113A ARG* 3.4 33.6 + - - +
114A ALA* 3.2 17.8 + - - +
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Residues in contact with ALA 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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74A VAL* 4.2 9.6 - - + +
96A LEU* 3.5 21.9 - - + +
99A CYS* 4.0 7.9 - - + -
100A SER* 3.8 30.3 - - - +
107A THR 2.8 13.2 + - - +
108A LYS 3.0 9.1 + - - +
110A ALA* 1.3 77.7 - - - +
112A PHE* 1.3 62.2 + - - +
114A ALA* 3.2 12.3 + - - +
115A VAL* 3.3 13.2 + - - +
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Residues in contact with PHE 112 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100A SER* 3.4 44.0 - - - -
108A LYS* 3.2 35.0 + - + +
109A GLN* 4.6 5.4 - - - +
111A ALA* 1.3 75.9 - - - +
113A ARG* 1.3 61.8 + - - +
115A VAL* 3.4 24.9 + - + +
116A PRO* 4.0 3.6 - - - +
128A PHE* 4.5 6.1 - + - -
132A LYS* 4.3 13.5 - - - -
147A ALA* 3.5 32.5 - - + +
148A LEU* 4.1 20.4 - - + -
151A ALA* 3.9 29.6 - - + +
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Residues in contact with ARG 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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71A CYS* 5.6 3.2 - - - +
74A VAL* 5.9 0.6 - - - +
78A LYS* 5.6 0.2 - - - -
106A LYS* 4.8 3.4 + - - +
109A GLN* 3.1 36.7 + - - +
110A ALA* 3.5 40.0 + - - +
111A ALA 3.1 0.4 - - - -
112A PHE* 1.3 80.6 - - - +
114A ALA* 1.3 58.7 + - + +
116A PRO* 3.6 14.4 - - - +
117A GLU* 5.0 3.8 - - - +
83B GLU* 4.6 20.5 + - - +
528B ASP* 5.2 4.0 + - - -
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Residues in contact with ALA 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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74A VAL* 4.2 11.0 - - + -
78A LYS* 3.6 38.8 - - + +
96A LEU* 4.7 3.6 - - + -
110A ALA 3.2 14.3 + - - +
111A ALA 3.2 6.2 + - - +
113A ARG* 1.3 76.9 - - - +
115A VAL* 1.3 62.7 + - - +
116A PRO* 3.4 3.4 - - - -
117A GLU* 3.1 6.7 + - - +
118A VAL* 3.1 28.4 + - + +
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Residues in contact with VAL 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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96A LEU* 3.8 17.3 - - + -
111A ALA 3.3 15.4 + - - +
112A PHE* 3.4 18.2 - - + +
114A ALA* 1.3 77.2 - - - +
116A PRO* 1.3 62.5 - - + +
118A VAL* 4.7 2.7 - - - -
119A CYS* 2.7 57.1 + - + +
125A LEU* 4.6 14.6 - - + -
128A PHE* 4.0 17.9 - - + -
151A ALA* 4.6 20.6 - - + +
155A TRP* 4.7 6.3 - - + -
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Residues in contact with PRO 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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112A PHE 4.0 3.8 - - - +
113A ARG 3.6 14.6 - - - +
114A ALA 3.4 2.7 - - - -
115A VAL* 1.3 97.0 - - + +
117A GLU* 1.3 66.8 + - + +
118A VAL 3.8 0.2 + - - -
119A CYS 3.8 11.4 - - - +
120A ARG* 4.6 5.7 + - - +
151A ALA* 5.8 2.0 - - + +
154A ASP* 5.6 5.8 - - + +
155A TRP* 4.2 26.9 + - + +
158A THR* 5.4 6.1 - - - +
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Residues in contact with GLU 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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78A LYS* 2.9 31.0 + - + -
82A GLN* 2.8 45.7 + - - +
113A ARG 5.0 2.4 - - - +
114A ALA* 3.1 10.5 + - - +
116A PRO* 1.3 87.4 - - + +
118A VAL* 1.3 60.1 + - - +
120A ARG* 2.9 25.0 + - - +
82B GLN* 3.4 22.3 - - - +
117B GLU* 4.7 1.0 - - - +
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Residues in contact with VAL 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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77A ILE* 4.6 6.3 - - + -
78A LYS* 4.0 31.2 - - + +
81A SER* 3.8 24.2 + - - +
89A GLN* 4.8 1.8 - - - +
92A THR* 5.4 3.8 - - - -
93A LEU* 3.9 21.6 - - + +
96A LEU* 3.8 29.8 - - + -
114A ALA* 3.1 17.1 + - + +
115A VAL 4.1 1.6 - - - +
117A GLU* 1.3 84.1 - - - +
119A CYS* 1.3 59.4 + - - +
120A ARG* 3.5 10.1 + - - +
124A HIS* 3.7 12.0 + - - +
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Residues in contact with CYS 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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93A LEU* 4.0 13.7 - - - -
96A LEU* 5.9 0.9 - - - -
115A VAL* 2.7 35.9 + - - +
116A PRO 3.8 7.2 - - - +
118A VAL* 1.3 76.4 - - - +
120A ARG* 1.3 58.6 + - - +
121A ILE 3.4 2.7 - - - -
124A HIS* 3.5 31.4 - - + -
125A LEU* 4.0 13.2 - - + +
128A PHE* 4.3 10.5 - - - -
155A TRP* 2.6 41.5 + - + +
159A LYS* 5.7 0.2 - - - -
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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