Contacts of the helix formed by residues 108 - 121 (chain B) in PDB entry 2AMT
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 HIS 108 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23B VAL* 3.7 25.5 - - + +
24B ARG 5.1 1.8 + - - -
25B ILE* 3.6 33.3 - - + +
26B PRO* 5.0 7.9 - - + -
104B LYS* 3.1 28.0 + - - +
105B MET* 2.9 11.5 + - - +
107B PRO* 1.3 94.6 - - + +
109B ILE* 1.3 64.0 + - - +
110B PRO 3.5 1.3 - - - -
111B GLN* 3.5 6.0 + - - -
112B MET* 3.3 32.5 + - + +
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Residues in contact with ILE 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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56A ASP* 5.4 1.3 - - - +
59A LYS* 6.3 0.9 - - - +
1901A 1AA 6.1 0.4 - - - +
98B ILE* 4.8 0.7 - - + -
105B MET* 3.4 16.4 - - + +
106B LEU* 3.5 35.9 - - + +
108B HIS* 1.3 75.7 - - - +
110B PRO* 1.4 70.5 - - + +
112B MET* 2.9 23.2 + - + +
113B ARG* 3.0 23.2 + - - +
129B VAL* 3.4 47.3 - - + +
130B LYS* 4.1 15.5 - - - -
131B ALA* 4.2 9.0 - - + +
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Residues in contact with PRO 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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59A LYS* 6.3 0.2 - - - +
106B LEU 3.4 14.6 - - - +
107B PRO* 3.5 14.8 - - + +
108B HIS 3.6 0.4 - - - -
109B ILE* 1.4 92.9 - - + +
111B GLN* 1.3 56.2 + - - +
113B ARG* 3.4 11.4 + - + +
114B VAL* 3.1 31.6 + - - +
124B MET* 4.9 0.9 - - - +
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Residues in contact with GLN 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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23B VAL* 3.7 15.7 - - + -
107B PRO 5.3 0.4 + - - -
108B HIS* 3.5 6.7 + - - +
109B ILE 3.2 0.6 - - - -
110B PRO* 1.3 78.2 - - - +
112B MET* 1.3 60.2 + - - +
114B VAL* 3.5 27.6 + - - +
115B PHE* 3.0 76.6 + - + -
118B GLU* 5.3 0.2 + - - -
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Residues in contact with MET 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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20B ILE* 3.4 44.6 - - + +
21B GLY* 3.4 18.6 - - - +
23B VAL* 3.7 3.6 - - + -
25B ILE* 4.3 5.8 - - + -
40B ALA* 5.5 0.4 - - - -
98B ILE* 3.8 25.4 - - + -
105B MET* 4.2 9.9 - - - +
108B HIS* 3.3 36.3 + - + +
109B ILE* 2.9 13.0 + - + +
111B GLN* 1.3 74.5 - - - +
113B ARG* 1.3 55.4 + - - +
115B PHE* 3.2 2.8 + - - +
116B ILE* 2.8 42.6 + - + +
129B VAL* 4.0 18.6 - - + -
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Residues in contact with ARG 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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53A ALA* 4.3 19.3 + - - +
59A LYS* 4.6 15.6 - - - +
109B ILE* 3.0 28.5 + - + +
110B PRO* 3.6 12.3 - - - +
112B MET* 1.3 75.8 - - - +
114B VAL* 1.3 56.5 + - - +
116B ILE* 4.0 0.7 - - - +
117B ALA* 2.9 33.1 + - - +
124B MET* 2.7 50.7 + - - +
125B ASP* 4.1 6.3 + - - +
127B VAL* 2.8 32.9 + - + +
128B ASN* 5.2 4.3 + - - -
129B VAL* 3.9 23.3 - - + +
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Residues in contact with VAL 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 PRO 3.1 17.0 + - - +
111B GLN* 3.5 34.3 - - - +
112B MET 3.2 0.2 - - - -
113B ARG* 1.3 76.8 - - - +
115B PHE* 1.3 61.6 + - - +
117B ALA* 3.9 1.6 - - - +
118B GLU* 3.1 47.2 + - + +
124B MET* 3.4 24.1 - - + +
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Residues in contact with PHE 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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21B GLY 3.8 7.2 - - - +
22B GLY* 3.3 35.0 - - - -
23B VAL* 3.7 9.4 - - + -
41B LEU* 6.3 0.4 - - + -
74B ARG* 3.2 48.0 + - - +
111B GLN* 3.0 54.0 + - + +
112B MET 3.2 4.0 + - - +
114B VAL* 1.3 76.2 - - - +
116B ILE* 1.3 64.1 + - + +
118B GLU* 3.5 11.7 + - - -
119B ASP* 3.2 21.2 + - - -
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Residues in contact with ILE 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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21B GLY* 4.8 5.6 - - - +
40B ALA* 6.0 2.9 - - + -
41B LEU* 3.8 26.2 - - + -
44B LEU* 3.6 28.9 - - + -
77B LEU* 4.9 3.6 - - + -
94B VAL* 4.5 1.3 - - + -
96B VAL* 4.9 5.4 - - + -
112B MET* 2.8 29.7 + - + +
115B PHE* 1.3 71.7 - - - +
117B ALA* 1.3 58.5 + - - +
119B ASP* 3.1 6.7 + - - +
120B LEU* 2.9 39.2 + - + +
127B VAL* 3.7 26.9 - - + -
129B VAL* 3.9 26.5 - - + -
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Residues in contact with ALA 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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113B ARG 2.9 19.9 + - - +
114B VAL 3.9 0.2 - - - +
116B ILE* 1.3 76.8 - - - +
118B GLU* 1.3 56.4 + - - +
121B GLY* 2.9 9.4 + - - -
122B CYS* 2.9 54.8 + - - +
123B HIS 3.9 12.1 - - - +
124B MET* 3.6 20.4 - - + -
127B VAL* 4.1 3.3 - - + +
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Residues in contact with GLU 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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74B ARG* 3.5 18.9 + - - +
111B GLN* 5.3 0.2 + - - -
114B VAL* 3.1 37.4 + - + +
115B PHE* 3.5 16.7 - - - +
116B ILE 3.2 0.2 - - - -
117B ALA* 1.3 76.5 - - - +
119B ASP* 1.3 61.8 + - - +
121B GLY* 3.4 10.6 + - - -
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Residues in contact with ASP 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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41B LEU* 5.5 0.3 - - - +
74B ARG* 2.8 56.4 + - - +
77B LEU* 3.7 24.8 - - + +
78B ARG* 3.1 40.6 + - + +
81B TRP* 3.5 17.5 - - - +
115B PHE 3.2 10.1 + - - +
116B ILE 3.1 8.1 + - - +
118B GLU* 1.3 78.1 - - - +
120B LEU* 1.3 60.7 + - - +
121B GLY 3.4 0.4 + - - -
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Residues in contact with LEU 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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44B LEU* 4.6 2.2 - - + -
48B LEU* 3.7 27.6 - - + -
77B LEU* 4.0 12.6 - - + -
81B TRP* 2.9 61.6 + - + +
85B GLN* 4.9 1.2 + - - -
91B LEU* 4.0 30.9 - - + +
94B VAL* 4.2 9.9 - - + -
116B ILE* 2.9 37.3 + - + +
119B ASP* 1.3 76.6 - - - +
121B GLY* 1.3 65.9 + - - +
122B CYS* 3.5 13.9 + - - +
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Residues in contact with GLY 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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81B TRP* 5.1 0.2 - - - -
117B ALA 2.9 8.4 + - - -
118B GLU* 3.4 7.4 + - - -
119B ASP 3.4 3.4 - - - -
120B LEU* 1.3 79.7 - - - +
122B CYS* 1.3 58.8 + - - +
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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