Contacts of the helix formed by residues 105 - 122 (chain A) in PDB entry 6EKK
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 TRP 105 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12A THR* 5.4 5.8 - - + -
86A PHE* 3.8 1.3 - - - -
103A LEU* 2.8 57.6 + - + +
104A PRO* 1.3 88.4 - - + +
106A PHE* 1.3 65.8 + - - +
107A GLU* 3.4 3.8 - - - -
108A VAL* 3.3 27.0 + - + -
109A PHE* 3.0 38.5 + + + -
135A LEU* 6.2 2.2 - - + -
138A LEU* 6.5 1.1 - - + -
140A ILE* 4.3 14.4 - - + -
141A PRO* 4.6 5.2 - - + -
155A PHE* 4.2 19.1 - + - -
157A VAL* 3.7 31.6 - - + -
158A PRO* 3.5 33.0 + - + +
160A THR* 4.6 9.4 - - + +
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Residues in contact with PHE 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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72A THR* 3.4 39.9 - - + -
84A PHE* 4.0 20.4 - + - -
86A PHE* 3.6 9.9 - + - -
104A PRO* 3.4 25.1 + - + -
105A TRP* 1.3 71.5 - - - +
107A GLU* 1.3 80.0 + - - +
109A PHE* 4.0 0.2 - - - -
110A TYR* 3.0 46.6 + - + -
169A ASN* 5.9 4.0 - - - -
170A ARG* 5.3 0.7 - - + -
171A ASN* 3.3 30.7 - - - +
212A HIS* 3.9 15.9 - + - -
404A EDO 4.1 3.6 - - - +
405A EDO 3.8 18.2 - - - -
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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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105A TRP* 3.4 0.9 - - - -
106A PHE* 1.3 89.3 + - - +
108A VAL* 1.3 64.3 + - + +
110A TYR* 4.0 5.9 - - - +
111A LYS* 3.2 23.7 + - - +
168A GLU 3.5 18.5 - - - +
169A ASN* 3.5 14.6 + - - -
170A ARG* 2.8 45.7 + - + +
171A ASN 4.6 0.3 + - - -
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Residues in contact with VAL 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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105A TRP* 3.3 31.1 + - + +
106A PHE 3.3 0.4 - - - -
107A GLU* 1.3 78.7 - - + +
109A PHE* 1.3 60.9 + - + +
111A LYS* 3.4 6.0 + - - +
112A LEU* 3.0 41.3 + - + +
135A LEU* 6.2 0.4 - - + -
149A LEU* 5.7 0.6 - - + +
155A PHE* 3.4 60.1 - - + -
156A THR 5.0 0.7 - - - +
158A PRO* 4.5 9.0 - - + -
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Residues in contact with PHE 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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12A THR* 3.5 25.6 - - - -
13A PHE* 4.5 0.2 - - + -
86A PHE* 3.3 38.4 - + + -
99A ILE* 3.7 37.0 - - + -
101A SER* 3.6 7.6 - - - -
103A LEU* 3.6 27.4 - - + -
105A TRP* 3.0 42.1 + + + +
108A VAL* 1.3 76.5 - - + +
110A TYR* 1.3 59.8 + - - +
112A LEU* 3.7 21.5 - - + +
113A LEU* 2.9 36.1 + - - +
135A LEU* 4.5 8.5 - - + -
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Residues in contact with TYR 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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70A ASN* 3.8 35.5 + - + +
71A PHE 3.5 13.7 - - - -
72A THR* 2.7 29.7 + - - -
86A PHE* 4.3 13.7 - + + -
87A CYS 4.0 4.5 - - - -
106A PHE* 3.0 29.0 + + + +
107A GLU 4.0 3.6 - - - +
109A PHE* 1.3 76.7 - - - +
111A LYS* 1.3 63.0 + - - +
113A LEU* 3.3 8.5 + - + +
114A ASN* 3.1 28.5 + - - +
170A ARG* 3.5 41.5 - - + +
404A EDO 2.9 40.5 + - - -
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Residues in contact with LYS 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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107A GLU 3.2 12.0 + - - +
108A VAL* 3.5 10.1 - - - +
109A PHE 3.2 0.4 - - - -
110A TYR* 1.3 78.1 - - - +
112A LEU* 1.3 65.8 + - - +
114A ASN* 3.1 28.9 + - - +
115A ILE* 3.1 33.2 + - + +
149A LEU* 3.6 26.5 - - + -
153A SER* 5.2 5.6 - - - -
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Residues in contact with LEU 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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99A ILE* 5.6 2.5 - - + -
108A VAL* 3.0 36.9 + - + +
109A PHE* 3.7 21.3 - - + +
111A LYS* 1.3 76.6 - - - +
113A LEU* 1.3 57.5 + - + +
115A ILE* 3.3 7.6 + - + +
116A LEU* 2.9 42.2 + - + +
131A LEU* 3.9 31.6 - - + -
135A LEU* 3.7 35.0 - - + -
149A LEU* 3.6 28.7 - - + -
155A PHE* 5.2 0.4 - - + -
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Residues in contact with LEU 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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16A TYR* 3.9 27.4 - - + -
70A ASN* 5.0 0.2 - - - +
86A PHE* 3.4 34.8 - - + +
87A CYS 3.8 17.9 - - - +
88A ARG* 3.9 15.1 - - + +
97A PHE* 3.8 21.0 - - + +
98A CYS 4.1 0.7 - - - +
99A ILE* 4.0 16.6 - - + -
109A PHE 2.9 23.7 + - - +
110A TYR* 3.5 9.9 - - + +
111A LYS 3.2 0.2 - - - -
112A LEU* 1.3 77.4 - - - +
114A ASN* 1.3 56.6 + - - +
116A LEU* 3.3 5.3 + - + +
117A ALA* 2.8 32.7 + - - +
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Residues in contact with ASN 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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69A GLN* 3.8 12.1 + - - +
70A ASN* 5.2 3.4 + - - -
88A ARG* 2.7 42.7 + - - +
110A TYR* 3.1 17.2 + - - +
111A LYS* 3.1 25.9 + - + +
113A LEU* 1.3 77.4 - - - +
115A ILE* 1.3 61.8 + - + +
117A ALA* 3.4 2.8 + - - +
118A ASP* 3.1 24.3 + - - +
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Residues in contact with ILE 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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111A LYS* 3.1 30.9 + - + +
112A LEU* 3.6 8.7 - - - +
114A ASN* 1.3 73.6 - - + +
116A LEU* 1.3 65.7 + - - +
118A ASP* 3.3 5.6 + - - +
119A TYR* 3.0 55.5 + - + +
131A LEU* 3.7 13.7 - - + -
149A LEU* 3.7 45.5 - - + +
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Residues in contact with LEU 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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16A TYR* 3.7 36.3 - - + +
99A ILE* 5.6 4.3 - - + -
112A LEU* 2.9 31.3 + - + +
113A LEU* 3.8 6.3 - - + +
115A ILE* 1.3 75.2 - - - +
117A ALA* 1.3 57.3 + - - +
119A TYR* 3.4 4.9 + - + +
120A THR* 2.8 33.4 + - - -
128A TRP* 3.6 30.6 - - + +
131A LEU* 3.9 23.6 - - + -
132A LEU* 3.8 33.0 - - + -
135A LEU* 6.1 0.9 - - + -
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Residues in contact with ALA 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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88A ARG* 3.8 33.4 - - - +
97A PHE* 4.1 28.4 - - + -
113A LEU 2.8 18.2 + - - +
114A ASN 3.7 5.2 - - - +
116A LEU* 1.3 77.8 - - - +
118A ASP* 1.3 56.4 + - - +
120A THR* 3.5 2.6 + - - -
121A THR* 2.9 31.7 + - - +
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Residues in contact with ASP 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 ASN 3.1 16.4 + - - +
115A ILE* 3.8 5.8 - - - +
116A LEU 3.3 0.2 - - - -
117A ALA* 1.3 74.9 - - - +
119A TYR* 1.3 66.1 + - - +
121A THR* 3.6 10.0 - - - +
122A LYS* 2.8 35.3 + - - +
124A GLN* 4.7 7.1 - - - +
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Residues in contact with TYR 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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115A ILE* 3.0 40.6 + - + +
116A LEU* 3.6 12.1 - - + +
118A ASP* 1.3 82.3 - - - +
120A THR* 1.3 55.3 + - - +
122A LYS 3.3 0.3 + - - -
123A ARG 2.9 9.5 + - - -
124A GLN* 2.7 67.0 + - - +
127A GLN* 3.5 36.8 - - + +
128A TRP* 3.6 26.2 - - + -
131A LEU* 4.2 8.9 - - + +
149A LEU 5.2 5.4 + - - -
150A SER* 5.8 3.3 - - - -
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Residues in contact with THR 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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16A TYR* 4.1 1.0 + - - -
35A ARG* 3.2 33.5 + - - +
97A PHE* 4.0 25.8 - - + -
116A LEU 2.8 21.6 + - - -
117A ALA 3.5 6.5 - - - -
119A TYR* 1.3 75.5 - - - +
121A THR* 1.3 63.3 + - - +
123A ARG* 3.1 13.4 + - - +
125A GLU* 5.0 0.7 - - - -
128A TRP* 3.8 10.8 + - - -
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Residues in contact with THR 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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97A PHE* 5.7 2.3 - - - -
117A ALA* 2.9 23.5 + - - +
118A ASP* 3.2 13.1 + - - +
120A THR* 1.3 79.2 - - - +
122A LYS* 1.3 60.0 + - + +
123A ARG* 3.1 7.3 + - - +
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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 ASP* 2.8 25.8 + - - +
121A THR* 1.3 71.7 - - + +
123A ARG* 1.3 69.9 + - - +
124A GLN* 3.1 27.4 + - + +
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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