Contacts of the helix formed by residues 106 - 123 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75A THR* 4.8 0.9 - - - +
103A ARG 3.8 3.7 - - - +
104A LEU* 3.2 3.3 - - - -
105A THR* 1.3 83.7 - - - +
107A LEU* 1.3 64.1 + - - +
108A GLN* 3.5 8.2 + - - +
109A TYR* 3.0 39.5 + - - +
110A PHE* 3.1 11.2 + - - +
141A LEU* 6.0 2.0 - - - -
17B TYR* 4.1 10.5 - - - -
52B GLU 4.8 8.5 - - - -
53B ARG 4.9 3.6 - - - -
55B GLY* 4.4 15.3 - - - -
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Residues in contact with LEU 107 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106A SER* 1.3 72.8 - - - +
108A GLN* 1.3 61.2 + - - +
110A PHE* 3.5 2.6 + - - -
111A SER* 3.2 17.0 + - - -
141A LEU* 4.1 26.9 - - + +
142A TYR* 4.7 2.0 - - - +
145A ARG* 4.3 6.5 - - - +
149A PHE* 4.9 2.2 - - + -
151A ILE* 3.6 38.8 - - + +
152A ASP* 3.6 19.3 - - - +
155A ILE* 3.5 27.0 - - + +
15B LEU* 3.6 36.8 - - + -
17B TYR* 5.0 2.2 + - - +
54B LEU 5.0 3.3 + - - +
55B GLY* 4.5 6.7 - - - +
56B VAL* 5.2 1.1 - - + -
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Residues in contact with GLN 108 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A THR* 3.8 26.2 + - + +
79A LYS* 2.7 39.3 + - - +
106A SER* 3.0 8.2 - - - +
107A LEU* 1.3 76.9 - - - +
109A TYR* 1.3 62.9 + - - +
111A SER* 3.3 5.7 + - - -
112A ILE* 3.2 25.9 + - - +
151A ILE* 3.2 20.0 - - - +
55B GLY* 3.0 32.4 + - - +
56B VAL 4.7 0.7 - - - -
57B ASN* 4.5 10.6 + - - +
7E VAL 4.6 0.9 + - - +
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Residues in contact with TYR 109 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A GLU* 2.9 35.3 + - + +
75A THR* 3.5 21.8 - - + -
78A GLU* 4.3 8.4 + - + -
99A ILE* 3.7 24.8 - - + +
102A LYS* 3.2 69.2 + - + +
103A ARG* 3.7 4.1 - - - +
105A THR* 4.4 10.8 - - + -
106A SER* 3.0 27.4 + - - +
108A GLN* 1.3 76.2 - - - +
110A PHE* 1.3 60.8 + - - +
112A ILE* 3.2 11.4 + - + +
113A TYR* 2.8 27.5 + - - +
52B GLU* 6.1 0.4 - - - -
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Residues in contact with PHE 110 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103A ARG 3.1 14.9 + - - +
104A LEU* 3.5 30.5 - - + -
106A SER 3.1 10.2 + - - +
107A LEU* 3.8 9.6 - - - +
108A GLN 3.3 0.4 - - - -
109A TYR* 1.3 74.6 - - - +
111A SER* 1.3 58.2 + - - +
113A TYR* 3.0 21.4 + + - +
114A LEU* 2.9 57.0 + - + +
134A ILE* 5.1 5.2 - - + -
137A ASP* 3.8 24.9 - - + -
138A LEU* 4.3 16.2 - - + -
141A LEU* 3.5 27.6 - - + -
155A ILE* 3.6 27.1 - - + -
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Residues in contact with SER 111 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A LYS* 4.9 1.8 - - - -
107A LEU 3.2 10.6 + - - -
108A GLN 3.6 9.2 - - - -
110A PHE* 1.3 79.0 - - - +
112A ILE* 1.3 62.5 + - - +
114A LEU* 3.4 11.0 + - - +
115A GLY 3.1 16.1 + - - -
151A ILE* 4.1 6.3 - - - -
154A GLU* 3.1 26.7 + - - +
155A ILE* 3.9 17.7 - - - +
158A ASN* 3.2 18.8 + - - +
6E PHE* 3.8 9.6 - - - -
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Residues in contact with ILE 112 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A THR* 3.6 29.4 - - + +
78A GLU* 3.3 35.4 - - + +
79A LYS* 3.8 19.3 - - + -
82A ILE* 3.8 15.2 - - + +
99A ILE* 4.1 10.5 - - + -
108A GLN 3.2 16.3 + - - +
109A TYR* 3.4 15.7 - - + +
110A PHE 3.1 0.6 - - - -
111A SER* 1.3 71.9 - - - +
113A TYR* 1.3 66.5 + - - +
115A GLY* 3.0 11.8 + - - -
116A TYR* 3.2 41.6 + - + -
6E PHE* 4.7 0.2 - - - -
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Residues in contact with TYR 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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96A PHE* 3.9 28.4 - + - -
99A ILE* 4.1 10.1 - - + +
100A GLU* 4.0 17.3 - - + -
103A ARG* 3.6 43.7 - - + -
109A TYR 2.8 13.2 + - - +
110A PHE* 3.1 26.5 - + - +
112A ILE* 1.3 75.8 - - - +
114A LEU* 1.3 68.5 + - + +
116A TYR* 3.1 16.7 + - - +
117A ILE* 3.2 23.2 + - + +
129A THR* 4.4 2.4 + - - -
130A PHE* 3.1 47.3 + + - -
133A THR* 4.0 7.6 + - - -
134A ILE* 5.4 0.7 - - + -
137A ASP* 4.5 3.4 - - - -
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Residues in contact with LEU 114 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110A PHE* 2.9 43.8 + - + +
111A SER* 3.7 7.2 - - - +
113A TYR* 1.3 90.9 - - + +
115A GLY* 1.3 64.8 + - - +
117A ILE* 3.4 5.6 + - + +
118A SER* 3.3 23.7 + - - -
130A PHE* 4.4 7.9 - - + -
134A ILE* 5.0 0.2 - - + -
155A ILE* 3.5 33.7 - - + +
158A ASN* 4.3 15.9 - - + +
159A LEU* 3.8 30.1 - - + +
162A VAL* 4.0 14.1 - - + +
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Residues in contact with GLY 115 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A ILE* 4.1 11.6 - - - +
86A PHE* 4.3 1.2 - - - -
111A SER 3.1 6.5 + - - -
112A ILE 3.0 9.5 + - - -
114A LEU* 1.3 78.1 - - - +
116A TYR* 1.3 60.6 + - - +
118A SER* 3.3 20.2 + - - -
119A ILE* 3.4 11.8 + - - +
158A ASN* 5.2 0.6 - - - +
4E LEU* 5.1 3.4 - - - -
6E PHE* 3.9 26.5 - - - -
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Residues in contact with TYR 116 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A GLU* 4.4 2.8 + - - -
81A LEU* 4.2 9.5 - - - +
82A ILE* 4.3 12.3 - - + -
85A ILE* 3.3 29.3 - - + +
92A PHE* 3.1 31.1 - + + -
95A ASN* 3.4 29.4 + - + +
96A PHE* 3.7 28.5 - + + -
98A ARG* 4.1 4.5 + - - -
99A ILE* 3.7 31.9 - - + +
112A ILE* 3.2 37.7 + - + -
113A TYR 3.1 8.2 + - - +
115A GLY* 1.3 73.7 - - - +
117A ILE* 1.3 60.4 + - - +
118A SER 3.0 1.8 - - - -
119A ILE* 2.8 24.4 + - + -
120A ALA 2.9 10.2 + - - -
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Residues in contact with ILE 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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96A PHE* 4.1 18.8 - - + -
113A TYR* 3.2 31.1 + - + +
114A LEU* 3.7 10.3 - - - +
115A GLY 3.4 0.2 - - - -
116A TYR* 1.3 76.8 - - - +
118A SER* 1.3 57.6 + - - +
120A ALA* 3.3 4.4 + - - +
121A HIS* 2.9 57.2 + - + +
127A VAL* 4.1 12.6 - - + -
130A PHE* 3.8 43.5 - - + -
162A VAL* 3.7 14.1 - - + -
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Residues in contact with SER 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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86A PHE* 4.1 6.8 - - - -
114A LEU 3.3 6.9 + - - -
115A GLY 3.3 12.0 + - - -
116A TYR 3.0 0.6 - - - -
117A ILE* 1.3 77.5 - - - +
119A ILE* 1.3 59.6 + - - +
121A HIS* 3.9 4.1 - - - +
122A HIS* 3.0 29.3 + - - +
158A ASN 4.6 0.3 + - - -
161A ASN* 3.7 16.4 + - - -
162A VAL* 3.0 24.1 - - - +
4E LEU* 3.9 25.9 - - - +
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Residues in contact with ILE 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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82A ILE* 3.6 33.4 - - + +
85A ILE* 3.6 31.0 - - + +
86A PHE* 3.5 31.0 - - + +
89A PRO* 5.2 1.3 - - + -
92A PHE* 3.8 18.8 - - + -
115A GLY 3.4 7.6 + - - +
116A TYR* 2.8 18.2 + - + +
118A SER* 1.3 74.5 - - - +
120A ALA* 1.3 59.9 + - - +
122A HIS* 3.2 1.4 + - - +
123A TYR* 2.9 53.2 + - + +
125A ILE* 5.8 0.9 - - + -
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Residues in contact with ALA 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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92A PHE* 3.5 17.6 - - + -
116A TYR 2.9 5.2 + - - +
117A ILE* 3.6 8.7 - - - +
119A ILE* 1.3 77.3 - - - +
121A HIS* 1.3 56.8 + - - +
123A TYR 3.4 0.5 + - - -
124A ASN 2.9 6.9 + - - -
125A ILE* 2.6 50.3 + - + +
127A VAL* 3.5 35.7 - - + -
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Residues in contact with HIS 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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117A ILE* 2.9 40.5 + - + +
118A SER* 3.9 5.6 - - - +
120A ALA* 1.3 76.1 - - - +
122A HIS* 1.3 63.6 + - - +
124A ASN* 3.3 18.6 + - - +
125A ILE 5.0 1.3 - - - -
127A VAL* 4.2 17.0 - - + +
130A PHE* 4.1 12.8 - + - -
131A ASN* 5.5 1.2 + - - -
161A ASN 4.7 2.6 + - - +
162A VAL* 3.7 33.2 - - + +
291A PRO* 5.6 13.1 - - + +
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Residues in contact with HIS 122 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A PHE* 4.3 12.7 - + + -
118A SER 3.0 18.4 + - - +
119A ILE 3.7 4.3 - - - +
121A HIS* 1.3 78.2 - - - +
123A TYR* 1.3 85.2 + + + +
124A ASN* 3.3 6.9 + - - -
291A PRO* 5.8 6.5 - - + +
292A PRO 3.5 14.9 + - - -
293A LYS* 3.1 33.9 + - + -
295A VAL* 3.2 27.5 - - + +
305A ILE* 5.9 5.4 - - + -
306A GLU* 6.0 1.3 - - - -
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Residues in contact with TYR 123 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A PHE* 2.7 33.9 + + - -
87A THR* 4.8 0.9 - - - -
89A PRO* 3.5 39.2 - - + +
119A ILE* 2.9 35.4 + - + +
122A HIS* 1.3 101.1 + + - +
124A ASN* 1.3 60.6 + - - +
125A ILE* 2.8 45.0 + - + +
305A ILE* 5.1 1.4 - - - +
306A GLU* 4.6 9.4 + - - -
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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
------------------------------------------------------------
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