Contacts of the helix formed by residues 106 - 123 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103C ARG 3.8 3.5 - - - +
104C LEU 3.2 2.9 - - - -
105C THR* 1.3 80.9 - - - +
107C LEU* 1.3 66.1 + - - +
108C GLN* 3.6 10.9 + - - +
109C TYR* 2.9 46.6 + - - +
110C PHE* 3.1 10.4 + - - +
141C LEU* 6.4 1.8 - - - -
17D TYR* 4.0 10.5 - - - -
52D GLU 4.8 8.1 - - - -
53D ARG 4.8 3.4 - - - -
55D GLY* 4.4 14.8 - - - -
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Residues in contact with LEU 107 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106C SER* 1.3 74.1 - - - +
108C GLN* 1.3 61.4 + - - +
110C PHE* 3.5 2.9 + - - -
111C SER 3.2 13.9 + - - -
141C LEU* 4.7 24.2 - - + +
142C TYR* 4.4 4.9 - - + +
145C ARG* 4.5 7.0 - - - +
149C PHE* 4.7 3.8 - - + -
151C ILE* 3.0 41.2 - - + +
152C ASP* 3.3 26.2 - - - +
155C ILE* 3.4 21.1 - - + +
15D LEU* 3.5 37.5 - - + -
17D TYR* 4.9 1.9 + - - +
54D LEU 4.9 2.6 + - - +
55D GLY* 4.5 6.5 - - - +
56D VAL* 5.2 1.6 - - + -
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Residues in contact with GLN 108 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73C ASN* 4.7 1.9 + - - +
75C THR* 2.9 43.2 + - + +
79C LYS* 5.0 6.6 + - - +
106C SER* 3.0 8.2 + - - +
107C LEU* 1.3 78.2 - - - +
109C TYR* 1.3 59.0 + - - +
111C SER* 3.3 6.3 + - - -
112C ILE* 3.0 27.8 + - - +
151C ILE* 4.0 11.4 - - + -
154C GLU* 5.9 0.2 - - - -
51D SER* 3.7 9.7 + - - +
52D GLU* 4.2 17.7 + - - +
55D GLY* 3.0 44.9 - - - +
56D VAL 4.0 3.5 + - - +
57D ASN* 5.5 1.0 - - - -
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Residues in contact with TYR 109 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74C GLU* 2.6 40.2 + - + -
75C THR* 3.9 17.5 - - + -
78C GLU* 5.0 6.7 - - + -
99C ILE* 4.3 13.3 - - + +
102C LYS* 3.1 43.5 + - + +
103C ARG* 3.7 3.7 - - - +
105C THR* 3.5 31.6 - - + -
106C SER* 2.9 28.7 + - - +
108C GLN* 1.3 76.4 - - - +
110C PHE* 1.3 59.4 + - - +
112C ILE* 3.2 22.1 + - + +
113C TYR* 2.8 28.1 + - - +
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Residues in contact with PHE 110 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103C ARG 3.1 22.7 + - - +
104C LEU* 4.0 8.5 - - + -
106C SER 3.1 9.3 + - - +
107C LEU* 3.6 9.9 - - - +
108C GLN 3.3 0.2 - - - -
109C TYR* 1.3 76.0 - - - +
111C SER* 1.3 57.5 + - - +
113C TYR* 3.1 31.4 + + - +
114C LEU* 2.9 45.2 + - + +
134C ILE* 5.5 3.8 - - + -
137C ASP* 3.7 30.3 - - + -
138C LEU* 4.7 7.9 - - + -
141C LEU* 3.4 35.4 - - + -
142C TYR* 5.2 4.0 - + - -
155C ILE* 3.6 35.4 - - + -
159C LEU* 6.1 3.6 - - + -
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Residues in contact with SER 111 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79C LYS* 6.0 1.1 - - - -
82C ILE* 4.9 0.9 - - - +
107C LEU 3.2 11.1 + - - -
108C GLN 3.6 9.0 - - - -
109C TYR 3.3 0.2 - - - -
110C PHE* 1.3 79.2 - - - +
112C ILE* 1.3 61.8 + - - +
114C LEU* 3.4 1.6 + - - -
115C GLY* 3.1 18.0 + - - -
151C ILE* 3.8 8.5 - - - -
154C GLU* 2.5 36.0 + - - +
155C ILE* 3.8 8.3 + - - +
158C ASN* 2.8 31.5 + - - +
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Residues in contact with ILE 112 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75C THR* 4.1 14.6 - - - +
78C GLU* 3.7 26.2 - - + -
79C LYS* 4.1 18.1 - - + +
82C ILE* 3.8 12.4 - - + +
99C ILE* 3.8 15.0 - - + -
108C GLN 3.0 19.9 + - - +
109C TYR* 3.2 33.0 - - + +
110C PHE 3.1 0.2 - - - -
111C SER* 1.3 76.4 - - - +
113C TYR* 1.3 63.2 + - - +
115C GLY* 3.0 10.7 + - - -
116C TYR* 2.9 46.3 + - + -
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Residues in contact with TYR 113 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96C PHE* 4.2 15.3 - + - -
99C ILE* 4.1 13.0 - - + +
100C GLU* 4.7 8.7 - - + -
103C ARG* 3.6 48.5 + - + -
109C TYR 2.8 13.9 + - - +
110C PHE* 3.1 29.6 - + - +
112C ILE* 1.3 77.2 - - - +
114C LEU* 1.3 71.6 + - + +
116C TYR* 3.1 14.5 + - - +
117C ILE* 3.2 30.2 + - + +
129C THR* 5.3 3.9 - - + +
130C PHE* 3.7 23.7 + + - -
133C THR* 3.3 22.0 + - - -
134C ILE* 4.5 3.5 - - + +
137C ASP* 3.8 8.0 + - - -
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Residues in contact with LEU 114 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110C PHE* 2.9 30.0 + - + +
111C SER 3.8 0.4 - - - +
112C ILE 3.3 0.4 - - - -
113C TYR* 1.3 93.9 - - + +
115C GLY* 1.3 65.5 + - - +
117C ILE* 3.4 6.3 + - + +
118C SER* 3.1 24.1 + - - -
130C PHE* 4.5 18.8 - - + -
134C ILE* 5.2 2.7 - - + -
155C ILE* 3.7 24.5 - - + +
158C ASN* 2.8 44.2 - - - +
159C LEU* 4.1 17.0 - - + -
161C ASN* 4.5 0.5 - - - +
162C VAL* 4.1 10.2 - - + +
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Residues in contact with GLY 115 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82C ILE* 4.2 21.0 - - - +
86C PHE* 4.2 1.2 - - - -
111C SER 3.1 10.3 + - - -
112C ILE 3.0 9.1 + - - -
114C LEU* 1.3 78.9 - - - +
116C TYR* 1.3 60.0 + - - +
118C SER* 3.3 16.7 - - - -
119C ILE* 3.2 16.8 - - - +
158C ASN* 4.7 4.7 + - - -
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Residues in contact with TYR 116 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78C GLU* 3.4 13.7 + - - +
81C LEU* 3.0 21.4 - - + +
82C ILE* 3.8 11.4 - - + -
85C ILE* 4.1 6.3 - - + -
92C PHE* 2.9 32.1 - + - -
95C ASN* 2.5 35.0 + - + -
96C PHE* 3.3 31.2 - + + -
99C ILE* 3.7 18.3 - - + +
112C ILE* 2.9 46.9 + - + +
113C TYR 3.1 4.3 + - - +
115C GLY* 1.3 73.2 - - - +
117C ILE* 1.3 59.2 + - - +
118C SER 3.0 2.2 - - - -
119C ILE* 2.8 40.1 + - + -
120C ALA 2.9 0.5 + - - -
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Residues in contact with ILE 117 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96C PHE* 3.6 27.6 - - + -
113C TYR* 3.2 25.9 + - + +
114C LEU* 3.7 11.4 - - - +
115C GLY 3.4 0.2 - - - -
116C TYR* 1.3 76.2 - - - +
118C SER* 1.3 57.1 + - - +
120C ALA* 3.3 4.5 + - - +
121C HIS* 2.9 60.6 + - + +
127C VAL* 4.4 8.5 - - + -
129C THR* 5.7 0.2 - - + -
130C PHE* 3.5 47.8 - - + +
162C VAL* 3.7 7.6 - - + -
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Residues in contact with SER 118 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86C PHE* 4.2 14.7 - - - -
114C LEU 3.1 10.1 + - - -
115C GLY* 3.3 13.3 + - - -
116C TYR 3.0 0.4 - - - -
117C ILE* 1.3 77.1 - - - +
119C ILE* 1.3 59.3 + - - +
121C HIS* 3.9 3.3 - - - +
122C HIS* 3.0 31.5 + - - +
158C ASN* 5.6 0.9 - - - +
161C ASN* 2.7 42.1 + - - +
162C VAL* 3.2 7.0 - - - +
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Residues in contact with ILE 119 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82C ILE* 4.1 8.3 - - + -
85C ILE* 3.9 24.7 - - + +
86C PHE* 3.2 30.1 - - + -
89C PRO* 5.3 0.2 - - + -
92C PHE* 3.4 18.8 - - + -
115C GLY 3.2 13.7 - - - +
116C TYR* 2.8 39.7 + - + +
118C SER* 1.3 76.0 - - - +
120C ALA* 1.3 61.2 + - - +
122C HIS* 3.2 2.7 + - - +
123C TYR* 2.9 60.9 + - + -
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Residues in contact with ALA 120 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92C PHE* 3.5 19.5 - - + -
116C TYR 2.9 5.2 + - - +
117C ILE 3.5 8.5 - - - +
119C ILE* 1.3 79.0 - - - +
121C HIS* 1.3 59.5 + - + +
123C TYR 3.4 0.3 + - - -
124C ASN 2.9 7.4 + - - -
125C ILE* 2.6 46.7 + - + +
127C VAL* 3.3 34.1 - - + -
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Residues in contact with HIS 121 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117C ILE* 2.9 45.5 + - + +
118C SER* 4.0 5.6 - - - +
120C ALA* 1.3 77.5 - - - +
122C HIS* 1.3 61.4 + - - +
124C ASN* 3.3 11.7 + - - +
125C ILE 5.0 1.8 - - - -
127C VAL* 3.7 24.6 - - + +
130C PHE* 3.9 11.6 - + - -
161C ASN 5.1 2.1 + - - +
162C VAL* 3.9 29.6 - - + +
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Residues in contact with HIS 122 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86C PHE* 4.1 26.1 - + + -
118C SER 3.0 17.7 + - - +
119C ILE* 3.6 7.0 - - - +
121C HIS* 1.3 77.1 - - - +
123C TYR* 1.3 72.3 + + + +
124C ASN* 3.3 0.9 + - - +
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Residues in contact with TYR 123 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85C ILE 4.0 1.3 - - - -
86C PHE* 2.4 37.8 + + - -
87C THR* 4.3 1.4 + - - -
89C PRO* 3.3 45.1 - - + +
92C PHE* 6.3 0.4 - + + -
119C ILE* 2.9 46.1 + - + +
122C HIS* 1.3 87.7 - - + +
124C ASN* 1.3 58.6 + - - +
125C ILE* 2.8 35.7 + - + +
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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