Contacts of the helix formed by residues 86 - 99 (chain B) in PDB entry 6B3I
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 86 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46B SER* 4.6 5.2 - - - -
50B GLN* 3.6 38.1 + - + +
85B ASP* 1.3 74.9 - - - +
87B PRO* 1.3 77.0 - - + +
88B SER* 4.2 10.3 - - - +
89B GLU* 2.9 52.1 + - + +
90B TYR* 3.0 11.6 + - - +
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Residues in contact with PRO 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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46B SER* 3.7 24.0 - - - +
85B ASP 4.1 1.8 - - - +
86B HIS* 1.3 88.6 - - + +
88B SER* 1.3 56.7 + - - +
90B TYR* 3.6 3.0 + - + +
91B ALA* 3.1 27.9 + - - +
273B VAL* 5.2 9.4 - - + +
274B THR* 4.0 29.1 - - + +
277B GLU* 6.3 0.9 - - + -
403B EDO 3.8 37.2 - - - +
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Residues in contact with SER 88 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86B HIS* 4.2 9.7 - - - +
87B PRO* 1.3 76.2 - - - +
89B GLU* 1.3 63.0 + - - +
91B ALA* 3.5 2.5 + - - +
92B ALA* 3.0 27.2 + - - +
120B GLU 4.8 0.2 - - - -
123B ALA* 3.6 44.3 + - - +
124B ILE* 3.8 16.5 - - - +
126B GLU* 5.5 0.9 + - - -
127B ALA* 3.8 7.2 - - - +
130B ARG* 5.6 0.2 + - - -
403B EDO 5.2 1.0 + - - -
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Residues in contact with GLU 89 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53B LYS* 5.4 3.3 + - - -
85B ASP* 3.8 17.7 - - + +
86B HIS* 2.9 50.4 + - + +
88B SER* 1.3 77.1 + - - +
90B TYR* 1.3 60.4 + - - +
92B ALA* 3.2 4.0 + - - +
93B ARG* 3.0 34.2 + - - +
127B ALA* 3.8 11.4 - - + -
130B ARG* 2.9 43.0 + - - +
131B LEU* 3.9 13.7 - - + +
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Residues in contact with TYR 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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78B LYS* 4.8 6.7 + - + +
82B ALA* 3.6 38.8 - - + +
85B ASP* 4.0 16.7 - - + +
86B HIS 3.0 14.1 + - - +
87B PRO* 4.1 4.7 - - + +
89B GLU* 1.3 73.0 - - - +
91B ALA* 1.3 60.2 + - - +
93B ARG* 3.3 13.4 + - + -
94B GLN* 2.9 49.2 + - + +
266B GLU* 3.1 24.3 + - - -
269B ILE* 3.5 17.6 - - + +
270B ARG* 3.7 24.3 + - - -
273B VAL* 4.2 6.7 - - + -
274B THR* 4.0 18.4 - - + -
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Residues in contact with ALA 91 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87B PRO 3.1 18.7 + - - +
88B SER* 3.7 5.4 - - - +
89B GLU 3.2 0.2 - - - -
90B TYR* 1.3 77.9 - - - +
92B ALA* 1.3 57.1 + - - +
94B GLN* 3.3 8.2 + - - +
95B LEU* 3.0 35.6 + - - +
112B VAL* 4.3 12.1 - - + +
116B ARG* 4.5 11.9 - - - +
124B ILE* 3.8 25.6 - - + -
270B ARG* 5.9 0.7 - - - -
274B THR* 4.6 5.1 - - + +
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Residues in contact with ALA 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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88B SER 3.0 15.3 + - - +
89B GLU 3.2 8.0 + - - +
91B ALA* 1.3 72.1 - - - +
93B ARG* 1.3 60.2 + - - +
95B LEU* 3.3 2.0 + - - +
96B GLN* 2.9 30.8 + - - +
124B ILE* 4.1 9.5 - - - +
127B ALA* 4.0 5.8 - - + -
128B TYR* 3.7 45.1 - - + +
131B LEU* 4.3 4.9 - - + -
132B PHE* 4.2 2.5 - - + -
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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
----------------------------------------------------------
65B GLU* 5.6 2.6 + - - -
85B ASP* 2.9 38.2 + - - -
89B GLU* 3.0 19.3 + - - +
90B TYR* 3.3 17.0 + - + +
92B ALA* 1.3 75.5 - - - +
94B GLN* 1.3 60.3 + - - +
96B GLN* 3.5 2.9 + - - +
97B LYS* 3.0 30.0 + - - +
131B LEU* 3.7 36.5 - - + +
132B PHE* 4.1 20.0 - - + -
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Residues in contact with GLN 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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90B TYR* 2.9 46.6 + - + +
91B ALA* 3.6 5.8 - - - +
93B ARG* 1.3 78.3 - - - +
95B LEU* 1.3 62.9 + - + +
97B LYS* 3.3 13.6 + - - +
98B ALA* 3.1 24.8 + - - +
108B VAL* 4.1 8.8 - - + +
112B VAL* 5.5 0.7 - - + -
266B GLU* 3.4 34.4 + - - +
270B ARG* 2.9 54.9 + - + +
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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
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91B ALA 3.0 20.8 + - - +
92B ALA* 3.3 4.7 + - - +
94B GLN* 1.3 75.7 - - - +
96B GLN* 1.3 62.4 + - - +
98B ALA* 3.2 13.2 + - + +
99B MET* 3.3 33.2 + - + +
108B VAL* 3.8 4.7 - - + +
109B LEU* 3.7 39.7 - - + +
112B VAL* 3.8 31.2 - - + -
113B LEU* 4.6 4.3 - - + -
124B ILE* 4.0 14.1 - - + -
128B TYR* 4.3 4.0 - - + -
136B LEU* 3.9 30.3 - - + -
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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
----------------------------------------------------------
92B ALA 2.9 17.9 + - - +
93B ARG 4.0 2.9 - - - +
95B LEU* 1.3 77.6 - - - +
97B LYS* 1.3 69.0 + - - +
98B ALA 3.4 0.3 + - - -
99B MET* 3.6 15.5 + - - +
100B LYS* 4.1 13.0 - - - +
128B TYR* 3.6 25.5 - - - +
132B PHE* 3.5 44.7 - - + -
134B ARG* 5.0 11.7 - - - +
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Residues in contact with LYS 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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78B LYS* 5.8 1.3 - - - +
93B ARG 3.0 19.0 + - - +
94B GLN* 3.7 14.8 - - - +
96B GLN* 1.3 83.4 + - - +
98B ALA* 1.3 58.1 + - - +
99B MET 3.4 0.2 - - - -
100B LYS* 3.3 24.6 - - - +
266B GLU* 3.9 26.1 + - - +
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Residues in contact with ALA 98 (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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94B GLN 3.1 17.4 + - - +
95B LEU* 3.2 5.1 + - - +
97B LYS* 1.3 78.0 - - - +
99B MET* 1.3 60.3 + - + +
100B LYS* 3.3 10.8 + - - +
104B THR* 4.5 2.1 + - - -
105B ASP 3.9 18.5 - - - +
106B GLU* 4.7 1.6 - - - +
108B VAL* 3.8 31.6 - - + +
109B LEU* 5.2 3.8 - - + +
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Residues in contact with MET 99 (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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95B LEU* 3.3 29.2 + - + +
96B GLN* 3.6 5.9 + - - +
97B LYS 3.4 1.6 - - - -
98B ALA* 1.3 74.8 - - + +
100B LYS* 1.3 74.2 + - - +
101B GLY 3.6 1.0 + - - -
106B GLU* 4.5 5.8 - - - +
109B LEU* 4.5 11.2 - - + -
128B TYR* 3.3 25.8 - - + +
136B LEU* 3.8 21.1 - - + -
139B ASP* 3.8 35.0 - - + +
140B VAL* 4.1 10.5 - - + -
143B ASP* 3.5 27.8 - - + +
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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