Contacts of the helix formed by residues 108 - 129 (chain A) in PDB entry 6YBO
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 108 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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100A LYS* 5.9 1.4 + - - -
101A ASP* 6.1 0.7 - - - +
106A ALA* 3.2 2.4 - - + +
107A ASN* 1.3 78.5 - - - +
109A ARG* 1.3 65.4 + - - +
110A ASP* 3.5 17.3 - - - +
111A VAL* 3.2 25.8 + - + +
112A ARG* 3.3 14.9 + - - +
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Residues in contact with ARG 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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107A ASN 3.4 4.4 + - - -
108A ASP* 1.3 72.7 - - - +
110A ASP* 1.3 64.0 + - - +
112A ARG* 3.1 33.8 + - + +
113A ARG* 3.1 63.1 + - + +
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Residues in contact with ASP 110 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108A ASP* 3.5 18.0 - - - +
109A ARG* 1.3 76.9 + - - +
111A VAL* 1.3 75.6 + - - +
113A ARG* 3.4 10.6 + - - +
114A TYR* 3.0 23.0 + - - +
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Residues in contact with VAL 111 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98A VAL* 3.7 40.8 - - + +
99A PHE* 4.1 11.7 - - + -
102A GLY 3.7 19.5 - - - +
103A GLY 4.5 0.9 - - - +
106A ALA* 3.8 9.2 - - + -
108A ASP* 3.2 21.3 + - + +
109A ARG 3.2 0.6 - - - -
110A ASP* 1.3 91.7 + - - +
112A ARG* 1.3 60.4 + - - +
114A TYR* 3.3 7.4 + - + +
115A ALA* 2.9 27.9 + - - +
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Residues in contact with ARG 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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103A GLY 3.4 20.2 - - - +
104A PHE* 3.2 23.9 - - - +
105A THR* 4.2 2.2 - - - +
106A ALA* 2.8 43.8 + - + +
107A ASN* 2.9 21.8 + - - +
108A ASP 3.3 3.3 + - - +
109A ARG* 3.1 39.1 + - - +
111A VAL* 1.3 76.8 - - - +
113A ARG* 1.3 62.5 + - + +
115A ALA* 3.4 3.3 + - - +
116A LEU* 3.1 30.8 + - + +
157A ARG* 3.5 34.0 - - - +
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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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109A ARG* 3.1 60.2 + - + +
110A ASP* 3.8 9.9 - - - +
112A ARG* 1.3 74.3 - - + +
114A TYR* 1.3 63.5 + - - +
116A LEU* 3.3 12.2 + - + +
117A ARG* 3.1 28.6 + - + +
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Residues in contact with TYR 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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61A PHE* 3.3 32.8 - + - -
98A VAL* 4.2 20.0 - - + -
99A PHE* 3.6 34.1 - + - -
110A ASP 3.0 17.0 + - - +
111A VAL* 3.3 6.0 + - - +
113A ARG* 1.3 73.7 - - - +
115A ALA* 1.3 59.3 + - - +
117A ARG* 3.1 9.1 + - + -
118A LYS* 2.9 43.6 + - + +
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Residues in contact with ALA 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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93A LEU* 4.1 13.6 - - + +
99A PHE* 4.0 10.1 - - + -
103A GLY* 3.7 31.6 - - - -
104A PHE* 4.0 10.3 - - + -
111A VAL 2.9 17.6 + - - +
112A ARG 3.6 5.2 - - - +
113A ARG 3.3 0.2 - - - -
114A TYR* 1.3 77.3 - - - +
116A LEU* 1.3 61.2 + - - +
118A LYS* 3.4 3.5 + - - +
119A THR* 2.9 29.3 + - - -
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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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104A PHE* 4.0 13.0 - - + -
112A ARG* 3.1 21.2 + - + +
113A ARG* 3.6 11.9 - - + +
114A TYR 3.2 0.2 - - - -
115A ALA* 1.3 77.2 - - - +
117A ARG* 1.3 58.4 + - + +
119A THR* 3.3 2.9 + - - -
120A ILE* 2.9 41.3 + - + +
160A GLU* 6.2 0.7 - - + -
161A ALA* 3.8 39.7 - - + +
164A LEU* 3.8 29.8 - - + -
165A LEU* 3.9 19.3 - - + -
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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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113A ARG* 3.1 19.4 + - + +
114A TYR* 3.1 12.1 + - + +
116A LEU* 1.3 77.5 - - + +
118A LYS* 1.3 63.5 + - - +
120A ILE* 3.4 16.0 + - - +
121A ARG* 3.1 23.9 + - - +
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Residues in contact with LYS 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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55A ASP* 2.8 30.9 + - - +
56A ASP* 3.0 25.7 + - - -
61A PHE* 3.9 23.3 - - - -
91A THR* 4.2 4.0 - - + +
92A ASN 2.9 23.2 + - - -
93A LEU* 4.1 5.4 - - + -
96A HIS* 6.3 0.2 - - - -
99A PHE* 4.0 25.4 - - + -
114A TYR* 2.9 31.7 + - + +
115A ALA* 3.8 5.6 - - - +
117A ARG* 1.3 75.7 - - - +
119A THR* 1.3 62.8 + - - +
121A ARG* 3.6 8.1 + - - +
122A ASN* 3.4 19.4 + - - +
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Residues in contact with THR 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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91A THR* 3.6 25.8 + - - +
93A LEU* 3.7 16.8 - - - +
104A PHE* 3.8 6.9 - - + -
115A ALA 2.9 19.0 + - - -
116A LEU* 3.3 7.2 + - - -
118A LYS* 1.3 74.7 - - - +
120A ILE* 1.3 65.4 + - - +
122A ASN* 3.0 5.9 + - - +
123A ILE* 2.9 23.9 + - + +
134A TYR* 3.8 13.6 + - + -
165A LEU* 4.0 30.5 - - + -
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Residues in contact with ILE 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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116A LEU* 2.9 31.5 + - + +
117A ARG* 3.4 17.2 + - - +
119A THR* 1.3 75.0 - - - +
121A ARG* 1.3 64.5 + - - +
123A ILE* 3.2 17.9 + - - +
124A ASP* 3.2 15.4 + - - +
164A LEU* 5.7 3.8 - - + +
165A LEU* 3.8 20.6 - - + -
168A TYR* 3.5 51.1 - - + +
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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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63A SER 5.1 9.1 + - - -
65A ASP* 3.2 26.9 + - - +
68A ARG* 3.5 55.5 + - - +
117A ARG 3.1 17.4 + - - +
118A LYS* 3.7 8.3 - - - +
119A THR 3.3 0.2 - - - -
120A ILE* 1.3 78.8 - - - +
122A ASN* 1.3 61.6 + - - +
124A ASP* 3.5 11.2 + - - +
125A LEU 3.4 13.3 + - - -
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Residues in contact with ASN 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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53A PHE* 3.7 22.1 - - - -
55A ASP* 3.3 33.3 - - + +
59A ILE* 5.3 0.2 - - - +
68A ARG* 5.0 2.6 + - - +
89A ALA* 4.2 1.4 - - - +
90A THR 2.9 29.3 + - - +
91A THR* 4.8 0.7 - - - +
118A LYS 3.4 8.5 + - - +
119A THR 3.0 5.1 + - - +
121A ARG* 1.3 79.8 - - - +
123A ILE* 1.3 59.3 + - - +
125A LEU* 3.2 14.9 + - - +
126A ALA* 2.8 28.2 + - - +
134A TYR* 3.1 21.6 + - - +
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Residues in contact with ILE 123 (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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119A THR* 2.9 22.8 + - + +
120A ILE* 3.2 12.3 + - + +
122A ASN* 1.3 76.2 - - - +
124A ASP* 1.3 62.0 + - - +
126A ALA* 3.2 2.2 + - - +
127A VAL* 3.0 27.8 + - + +
134A TYR* 3.9 27.4 - - + -
165A LEU* 4.0 23.1 - - + -
168A TYR* 4.5 6.7 - - + -
169A VAL* 4.0 22.4 - - + -
174A TYR* 4.0 16.6 - - + -
176A ILE* 4.6 7.9 - - + -
178A PHE* 3.9 26.2 - - + -
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Residues in contact with ASP 124 (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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120A ILE* 3.2 11.6 + - - +
121A ARG* 3.5 12.6 - - - +
122A ASN 3.2 0.2 - - - -
123A ILE* 1.3 79.1 - - - +
125A LEU* 1.3 61.9 + - - +
127A VAL* 3.4 3.5 + - - +
128A GLU* 3.1 22.8 + - - +
168A TYR* 2.6 30.3 + - - -
172A GLN* 5.6 0.2 - - - -
174A TYR* 2.7 32.5 + - - +
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Residues in contact with LEU 125 (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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53A PHE* 4.1 13.2 - - + -
58A LEU* 4.3 3.6 - - + -
59A ILE* 3.6 31.2 - - + -
68A ARG* 4.1 12.8 - - - +
72A VAL* 4.0 31.2 - - + -
121A ARG 3.4 8.1 + - - +
122A ASN* 3.2 24.1 + - - +
124A ASP* 1.3 76.5 - - - +
126A ALA* 1.3 67.3 + - - +
128A GLU* 3.1 21.0 + - - +
129A LEU* 3.0 34.0 + - + +
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Residues in contact with ALA 126 (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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53A PHE* 4.6 6.0 - - - -
89A ALA* 3.7 28.9 - - + -
122A ASN 2.8 17.4 + - - +
123A ILE 3.2 4.5 + - - +
125A LEU* 1.3 76.5 - - - +
127A VAL* 1.3 60.4 + - - +
129A LEU* 3.2 5.1 + - - +
130A GLY 3.1 5.0 + - - -
131A ALA* 3.0 36.1 + - + +
134A TYR* 3.9 15.3 - - + -
176A ILE* 4.3 4.0 - - + -
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Residues in contact with VAL 127 (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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123A ILE 3.0 17.2 + - - +
124A ASP 3.8 3.6 - - - +
126A ALA* 1.3 75.2 - - - +
128A GLU* 1.3 64.8 + - - +
130A GLY* 3.0 13.7 + - - +
131A ALA 4.7 6.3 - - - +
174A TYR* 3.7 54.7 - - + -
175A ASP 5.6 1.3 - - - +
176A ILE* 4.2 21.1 - - + -
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Residues in contact with GLU 128 (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 VAL* 4.3 15.8 - - - +
76A ARG* 3.3 36.7 + - - +
124A ASP 3.1 14.6 + - - +
125A LEU* 3.1 25.8 + - + +
127A VAL* 1.3 78.2 - - - +
129A LEU* 1.3 61.1 + - + +
130A GLY 3.5 0.5 + - - -
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Residues in contact with LEU 129 (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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53A PHE* 3.7 33.2 - - + -
58A LEU* 4.5 3.8 - - + -
72A VAL* 4.7 5.6 - - + -
75A PHE* 4.2 19.1 - - + -
76A ARG* 3.6 48.4 + - + +
79A LEU* 4.4 13.8 - - + +
86A VAL* 4.0 26.5 + - + +
125A LEU* 3.0 29.9 + - + +
126A ALA* 3.8 4.7 - - - +
127A VAL 3.2 0.2 - - - -
128A GLU* 1.3 76.6 - - + +
130A GLY* 1.3 59.6 + - - +
131A ALA 3.6 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