Contacts of the helix formed by residues 106 - 123 (chain B) in PDB entry 2AXZ
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 SER 106 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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17A TYR* 4.1 10.5 - - - -
52A GLU 4.9 7.0 - - - -
53A ARG 5.0 2.7 - - - -
54A LEU 4.9 0.4 - - - -
55A GLY* 4.4 15.9 - - - -
75B THR* 4.8 1.0 - - - +
103B ARG 3.8 4.2 - - - +
104B LEU 3.2 3.1 - - - -
105B THR* 1.3 82.7 + - - +
107B LEU* 1.3 66.0 + - - +
108B GLN* 3.6 8.1 + - - +
109B TYR* 3.0 39.2 + - - +
110B PHE* 3.1 10.6 + - - +
141B LEU* 6.1 2.0 - - - -
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Residues in contact with LEU 107 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A LEU* 3.8 33.4 - - + -
17A TYR* 5.1 0.6 + - - -
54A LEU 5.0 2.7 + - - +
55A GLY* 4.6 7.1 - - - +
56A VAL* 5.3 1.8 - - + -
106B SER* 1.3 73.0 - - - +
108B GLN* 1.3 61.4 + - - +
110B PHE* 3.5 2.8 + - - -
111B SER* 3.2 17.0 + - - -
141B LEU* 4.3 25.8 - - + +
142B TYR* 4.6 2.7 - - + +
145B ARG* 4.1 7.2 - - - +
149B PHE* 4.9 2.2 - - + -
151B ILE* 3.4 36.3 - - + +
152B ASP* 3.3 27.1 - - - +
155B ILE* 3.5 25.3 - - + +
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Residues in contact with GLN 108 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A GLY* 3.0 36.5 - - - +
56A VAL 4.7 0.2 - - - -
57A ASN* 4.4 11.3 + - - +
75B THR* 3.9 26.0 + - + +
79B LYS* 2.6 40.2 + - - +
106B SER* 3.0 8.2 - - - +
107B LEU* 1.3 77.5 - - - +
109B TYR* 1.3 61.6 + - - +
111B SER* 3.3 6.2 + - - -
112B ILE* 3.2 26.1 + - - +
151B ILE* 3.4 18.3 - - - +
7F VAL 5.2 0.3 - - - +
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Residues in contact with TYR 109 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74B GLU* 2.8 46.0 + - - +
75B THR* 3.6 13.5 - - + -
78B GLU* 4.5 13.5 + - + +
98B ARG* 5.6 0.3 + - - -
99B ILE* 3.8 29.3 - - + +
102B LYS* 3.2 52.8 + - + +
103B ARG* 3.7 4.0 - - - +
105B THR* 3.2 21.8 - - - +
106B SER* 3.0 21.9 + - - +
108B GLN* 1.3 77.0 - - - +
110B PHE* 1.3 60.6 + - - +
112B ILE* 3.2 11.3 + - + +
113B TYR* 2.8 27.5 + - - +
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Residues in contact with PHE 110 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103B ARG* 3.1 21.8 + - + +
104B LEU* 4.0 6.3 - - + -
106B SER 3.1 9.7 + - - +
107B LEU* 3.7 9.2 - - - +
108B GLN 3.3 0.2 - - - -
109B TYR* 1.3 76.0 - - - +
111B SER* 1.3 58.9 + - - +
113B TYR* 3.0 26.8 + + - +
114B LEU* 2.9 47.7 + - + +
134B ILE* 5.2 4.7 - - + -
137B ASP* 3.9 28.5 - - + -
138B LEU* 4.3 17.5 - - + -
141B LEU* 3.4 36.6 - - + -
155B ILE* 3.5 35.2 - - + -
159B LEU* 5.3 0.2 - - + -
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Residues in contact with SER 111 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79B LYS* 5.1 2.0 - - - -
107B LEU 3.2 10.2 + - - -
108B GLN 3.6 8.7 - - - -
109B TYR 3.3 0.2 - - - -
110B PHE* 1.3 79.6 - - - +
112B ILE* 1.3 63.1 + - - +
114B LEU* 3.4 9.8 + - - +
115B GLY 3.1 16.5 + - - -
151B ILE* 4.0 6.7 - - - -
154B GLU* 3.1 23.2 + - - +
155B ILE* 3.9 16.8 + - - -
158B ASN* 3.0 25.6 + - - +
6F PHE* 3.8 9.7 - - - -
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Residues in contact with ILE 112 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75B THR* 3.5 26.5 - - + +
78B GLU* 3.3 32.1 - - + -
79B LYS* 3.8 19.3 - - + -
82B ILE* 3.9 15.3 - - + +
99B ILE* 3.9 14.8 - - + -
108B GLN 3.2 16.3 + - - +
109B TYR* 3.4 17.3 - - + +
110B PHE 3.2 0.2 - - - -
111B SER* 1.3 75.1 - - - +
113B TYR* 1.3 65.5 + - - +
115B GLY* 3.0 11.4 + - - -
116B TYR* 3.1 41.7 + - + -
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Residues in contact with TYR 113 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96B PHE* 3.8 31.5 - + - -
99B ILE* 4.1 9.4 - - + -
100B GLU* 3.9 15.0 - - + -
103B ARG* 3.6 44.8 - - + -
109B TYR 2.8 13.4 + - - +
110B PHE* 3.1 25.8 - + - +
112B ILE* 1.3 77.1 - - - +
114B LEU* 1.3 67.0 + - + +
116B TYR* 3.1 15.3 + - - +
117B ILE* 3.2 24.9 + - + +
129B THR* 4.1 5.9 + - - -
130B PHE* 3.5 42.6 + + - -
133B THR* 3.7 8.3 + - - -
134B ILE* 5.6 0.9 - - + -
137B ASP* 4.4 6.3 - - - -
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Residues in contact with LEU 114 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110B PHE* 2.9 43.0 + - + +
111B SER* 3.7 7.4 - - - +
113B TYR* 1.3 83.0 - - + +
115B GLY* 1.3 64.7 + - - +
117B ILE* 3.4 5.6 + - - +
118B SER* 3.3 24.4 + - - -
130B PHE* 4.3 16.6 - - + -
155B ILE* 3.5 31.2 - - + +
158B ASN* 4.3 14.2 - - + +
159B LEU* 3.8 32.8 - - + +
162B VAL* 4.0 15.4 - - + +
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Residues in contact with GLY 115 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82B ILE* 4.1 12.1 - - - +
86B PHE* 4.5 1.6 - - - -
111B SER 3.1 10.1 + - - -
112B ILE 3.0 9.5 + - - -
114B LEU* 1.3 78.0 - - - +
116B TYR* 1.3 60.3 + - - +
118B SER* 3.3 20.0 + - - -
119B ILE* 3.4 12.1 + - - +
158B ASN* 5.2 2.4 - - - +
4F LEU* 5.2 2.7 - - - -
6F PHE* 3.9 22.7 - - - -
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Residues in contact with TYR 116 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78B GLU* 4.0 15.4 + - - -
81B LEU* 3.7 15.2 - - - +
82B ILE* 4.3 11.9 - - + -
85B ILE* 3.2 26.2 - - + -
92B PHE* 3.4 26.1 - + + -
95B ASN* 3.7 20.8 - - + +
96B PHE* 3.6 26.7 - + + -
98B ARG* 4.3 0.3 + - - -
99B ILE* 3.5 32.7 - - + +
112B ILE* 3.1 38.7 + - + -
113B TYR 3.1 7.7 + - - +
115B GLY* 1.3 72.8 - - - +
117B ILE* 1.3 60.0 + - - +
118B SER 3.0 1.6 - - - -
119B ILE* 2.8 30.6 + - + +
120B ALA 2.9 10.4 + - - -
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Residues in contact with ILE 117 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96B PHE* 4.2 13.7 - - + -
113B TYR* 3.2 37.7 + - + +
114B LEU* 3.6 11.2 - - - +
115B GLY 3.4 0.2 - - - -
116B TYR* 1.3 75.7 - - - +
118B SER* 1.3 57.7 + - - +
120B ALA* 3.3 5.5 + - - +
121B HIS* 2.9 48.3 + - + +
127B VAL* 4.4 9.6 - - + -
130B PHE* 3.6 44.9 - - + -
162B VAL* 3.7 21.3 - - + -
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Residues in contact with SER 118 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86B PHE* 4.1 7.3 - - - -
114B LEU 3.3 7.7 + - - -
115B GLY 3.3 12.3 + - - -
116B TYR 3.0 0.4 - - - -
117B ILE* 1.3 78.6 - - - +
119B ILE* 1.3 59.5 + - - +
121B HIS* 3.6 4.0 + - - +
122B HIS* 3.0 29.1 + - - +
158B ASN 4.5 0.7 + - - -
161B ASN* 3.3 16.5 + - - -
162B VAL* 3.1 23.5 - - - +
295B VAL* 5.9 0.2 - - - +
4F LEU* 3.9 26.7 - - - +
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Residues in contact with ILE 119 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82B ILE* 3.7 25.1 - - + +
85B ILE* 3.5 46.4 - - + +
86B PHE* 3.8 25.8 - - + +
89B PRO* 5.2 0.4 - - + -
92B PHE* 4.1 11.7 - - + -
115B GLY 3.5 11.9 - - - +
116B TYR* 2.8 22.0 + - + +
118B SER* 1.3 75.6 - - - +
120B ALA* 1.3 59.0 - - - +
122B HIS* 3.2 2.4 + - - +
123B TYR* 2.9 49.0 + - + +
125B ILE* 4.9 2.5 - - + -
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Residues in contact with ALA 120 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92B PHE* 3.7 14.1 - - + -
116B TYR 2.9 5.9 + - - +
117B ILE* 3.5 8.5 - - - +
119B ILE* 1.3 78.1 - - - +
121B HIS* 1.3 56.9 + - - +
123B TYR 3.4 0.3 + - - -
124B ASN 2.9 7.8 + - - -
125B ILE* 2.6 52.9 + - + +
127B VAL* 3.6 34.8 - - + -
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Residues in contact with HIS 121 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117B ILE* 2.9 35.7 + - + +
118B SER* 3.9 5.6 - - - +
120B ALA* 1.3 77.4 - - - +
122B HIS* 1.3 63.3 + - - +
124B ASN* 3.3 20.6 + - - +
125B ILE 5.1 1.6 - - - -
127B VAL* 4.3 15.0 - - + +
130B PHE* 4.4 12.4 - + - -
131B ASN* 5.3 2.4 + - - -
161B ASN* 4.7 3.1 + - - +
162B VAL* 3.6 37.8 - - + +
291B PRO* 5.3 15.8 - - + +
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Residues in contact with HIS 122 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86B PHE* 4.2 12.3 - + + -
118B SER 3.0 19.5 + - - +
119B ILE 3.2 4.0 + - - +
121B HIS* 1.3 77.5 - - - +
123B TYR* 1.3 90.2 - + - +
124B ASN* 3.3 5.5 + - - -
291B PRO* 6.2 4.7 - - + -
292B PRO 3.7 15.3 - - - -
293B LYS* 3.0 27.9 + - + +
295B VAL* 3.3 27.8 - - + +
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Residues in contact with TYR 123 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86B PHE* 2.8 33.7 + + - -
87B THR* 4.7 1.2 - - - -
89B PRO* 3.4 43.3 - - + +
119B ILE* 2.9 33.0 + - + +
122B HIS* 1.3 104.3 + + + +
124B ASN* 1.3 59.9 + - - +
125B ILE* 2.8 32.9 + - + +
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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
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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