Contacts of the helix formed by residues 84 - 98 (chain B) in PDB entry 4AE6
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 GLN 84 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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54B PHE* 3.8 35.8 - - + -
79B VAL* 3.0 16.3 + - + +
82B LEU* 3.3 25.0 + - + +
83B LYS* 1.3 80.3 + - - +
85B ILE* 1.3 64.6 + - - +
86B GLU 3.4 1.8 - - - -
87B HIS* 2.7 40.3 + - + +
88B THR* 2.7 30.5 + - - +
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Residues in contact with ILE 85 (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 VAL* 3.7 7.5 - - + +
80B VAL* 3.6 46.7 - - + +
83B LYS* 3.5 3.6 - - - -
84B GLN* 1.3 79.5 - - - +
86B GLU* 1.3 60.6 + - + +
88B THR* 3.6 1.7 - - - -
89B LEU* 2.8 48.5 + - + +
346B GLU* 3.9 28.9 - - + +
347B PHE* 4.0 13.4 - - + -
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Residues in contact with GLU 86 (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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83B LYS 5.6 0.2 + - - -
84B GLN 3.4 0.4 - - - -
85B ILE* 1.3 78.7 - - + +
87B HIS* 1.3 68.1 + - + +
89B LEU* 3.8 8.4 - - + +
90B ASN* 2.7 52.3 + - - +
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Residues in contact with HIS 87 (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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83B LYS 4.7 5.8 - - - -
84B GLN* 2.7 42.9 + - + +
85B ILE 3.3 0.4 - - - -
86B GLU* 1.3 87.3 - - + +
88B THR* 1.3 54.2 + - - +
90B ASN* 3.7 0.2 - - - +
91B GLU* 2.8 37.0 + - - +
186B GLY* 3.6 24.6 - - - -
187B PHE* 3.1 43.7 - + - -
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Residues in contact with THR 88 (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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54B PHE* 4.5 10.4 - - - -
74B LEU* 3.8 18.8 - - + -
79B VAL* 3.6 14.2 - - + +
84B GLN* 2.7 26.4 + - - +
85B ILE* 3.6 4.0 - - - -
87B HIS* 1.3 73.0 - - - +
89B LEU* 1.3 67.8 + - - +
91B GLU* 3.9 6.1 - - - +
92B LYS* 3.1 23.9 + - - +
116B LEU* 3.7 30.1 - - + -
118B MET* 5.3 3.6 - - - +
347B PHE* 4.8 2.0 - - + -
350B PHE* 4.5 8.3 - - + -
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Residues in contact with LEU 89 (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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85B ILE* 2.8 31.9 + - + +
86B GLU* 3.8 7.4 - - - +
88B THR* 1.3 79.3 - - - +
90B ASN* 1.3 56.4 + - - +
92B LYS* 3.4 6.0 + - - +
93B ARG* 2.9 29.8 + - - +
346B GLU 3.8 17.7 - - - +
347B PHE* 4.3 16.4 - - + -
349B GLU* 4.4 21.5 - - + +
350B PHE* 3.7 42.8 - - + +
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Residues in contact with ASN 90 (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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30B TRP* 5.1 6.9 - - - -
86B GLU* 2.7 36.9 + - - +
87B HIS 3.7 3.1 - - - +
89B LEU* 1.3 72.4 - - - +
91B GLU* 1.3 64.9 + - - +
93B ARG* 3.1 10.0 + - - +
94B ILE* 2.9 35.2 + - - +
185B PHE 3.2 13.3 + - - -
186B GLY 3.0 21.5 + - - +
187B PHE 4.1 0.2 - - - -
188B ALA 2.8 28.1 + - - +
189B LYS* 5.5 1.0 - - - +
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Residues in contact with GLU 91 (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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72B LYS* 4.4 15.4 + - - -
87B HIS 2.8 21.6 + - - +
88B THR* 3.9 6.4 - - - +
90B ASN* 1.3 76.1 - - - +
92B LYS* 1.3 57.3 + - - +
94B ILE* 3.8 0.7 - - - +
95B LEU* 2.8 56.1 + - + +
118B MET* 4.3 11.4 - - + +
183B THR 4.6 3.4 - - - -
184B ASP* 3.5 20.7 - - - +
185B PHE* 2.9 38.5 + - + +
186B GLY* 3.5 10.6 + - - +
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Residues in contact with LYS 92 (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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33B PRO* 4.5 10.5 - - - +
34B ALA 2.7 26.2 + - - -
35B GLN* 4.0 1.6 - - - +
88B THR 3.1 15.3 + - - +
89B LEU* 3.8 4.0 - - + +
91B GLU* 1.3 79.8 - - - +
93B ARG* 1.3 67.3 + - + +
95B LEU* 4.7 0.2 - - - -
96B GLN* 3.0 36.2 + - - +
106B LEU* 4.0 11.9 - - + +
109B SER* 3.2 23.6 - - - +
118B MET* 4.0 14.6 - - + -
349B GLU 4.0 6.6 + - - +
350B PHE* 2.8 60.6 + - + +
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Residues in contact with ARG 93 (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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30B TRP* 3.2 71.8 + - + +
31B GLU* 5.5 1.8 + - - +
33B PRO* 4.3 15.0 - - + +
89B LEU 2.9 19.5 + - - +
90B ASN* 3.1 11.3 + - - +
92B LYS* 1.3 80.2 - - + +
94B ILE* 1.3 63.0 + - - +
96B GLN* 2.7 40.7 + - - +
97B ALA* 3.5 4.7 + - - +
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Residues in contact with ILE 94 (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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26B PHE* 5.6 0.2 - - - -
30B TRP* 3.8 23.8 - - + -
90B ASN* 2.9 45.4 + - - +
91B GLU 4.0 2.2 - - - +
93B ARG* 1.3 75.9 - - - +
95B LEU* 1.3 66.6 + - - +
97B ALA* 2.9 13.3 + - - +
98B VAL* 3.1 33.3 + - + +
162B LEU* 4.2 20.2 - - + -
185B PHE* 3.8 29.2 - - + +
188B ALA* 3.6 27.1 - - + +
189B LYS* 5.2 0.4 - - - -
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Residues in contact with LEU 95 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B LYS* 6.2 0.7 - - - +
91B GLU* 2.8 44.9 + - + +
94B ILE* 1.3 73.0 - - - +
96B GLN* 1.3 60.7 + - - +
97B ALA 3.4 0.3 + - - -
98B VAL* 3.8 23.4 + - + +
103B LEU* 5.6 0.2 - - + -
104B VAL* 3.6 30.8 - - + +
106B LEU* 3.8 28.1 + - + +
118B MET* 3.7 16.8 - - + -
120B MET* 3.8 17.5 - - + -
183B THR 5.1 2.2 - - - +
185B PHE* 3.7 31.6 - - + -
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Residues in contact with GLN 96 (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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29B LYS* 3.4 41.3 + - - +
30B TRP* 4.2 1.6 - - - +
33B PRO* 3.4 34.0 - - + +
34B ALA* 3.4 14.5 + - + +
92B LYS* 3.0 41.4 + - - +
93B ARG* 2.7 27.4 + - - +
95B LEU* 1.3 77.8 - - - +
97B ALA* 1.3 66.5 + - - +
98B VAL 3.7 2.0 - - - +
106B LEU* 3.8 18.3 - - + +
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Residues in contact with ALA 97 (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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25B ASP 4.9 0.2 - - - -
26B PHE* 3.3 47.3 - - + +
29B LYS* 3.8 24.5 - - + +
30B TRP* 4.0 10.1 - - + +
93B ARG 3.5 11.1 + - - +
94B ILE 2.9 6.0 + - - +
96B GLN* 1.3 91.0 - - - +
98B VAL* 1.4 58.0 + - - +
156B TYR* 4.7 0.2 + - - -
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Residues in contact with VAL 98 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B PHE* 4.0 16.6 - - + -
94B ILE* 3.1 32.5 + - + +
95B LEU* 3.9 26.7 - - + +
96B GLN 3.7 1.8 - - - +
97B ALA* 1.4 79.5 - - - +
99B ASN* 1.3 64.9 + - - +
103B LEU* 3.6 25.4 - - + -
104B VAL 5.5 1.6 - - - +
105B LYS* 6.1 1.7 - - - +
156B TYR* 3.5 16.2 - - + +
157B LEU* 4.6 3.8 - - + -
160B LEU* 4.1 8.3 - - + -
162B LEU* 4.2 5.6 - - + -
185B PHE* 5.4 1.1 - - + -
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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