Contacts of the helix formed by residues 84 - 98 (chain L) in PDB entry 3E8E
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 L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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54L PHE* 3.8 35.7 - - + -
79L VAL* 2.8 21.2 + - + +
82L LEU* 3.6 15.2 + - + +
83L LYS* 1.3 72.4 + - - +
85L ILE* 1.3 63.5 + - - +
86L GLU 3.5 2.0 - - - -
87L HIS* 2.7 38.1 + - + +
88L THR* 3.2 27.1 + - + +
187L PHE* 3.7 9.9 - - - -
23N HIS* 3.3 10.1 - - - +
24N ASP* 2.8 44.8 + - - +
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Residues in contact with ILE 85 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79L VAL* 3.5 10.8 - - + +
80L VAL* 3.6 50.7 - - + +
83L LYS* 3.5 5.5 + - - -
84L GLN* 1.3 77.4 - - - +
86L GLU* 1.3 62.4 + - - +
88L THR* 2.8 19.5 + - - -
89L LEU* 3.3 19.8 + - + +
346L GLU* 3.7 31.2 - - + +
347L PHE* 3.5 18.4 - - + -
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Residues in contact with GLU 86 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83L LYS 6.2 0.2 - - - +
84L GLN 3.5 0.2 - - - -
85L ILE* 1.3 80.1 - - - +
87L HIS* 1.3 60.9 + - + +
89L LEU* 3.3 13.3 + - + +
90L ASN* 2.9 43.6 + - - +
189L LYS* 4.0 21.7 + - - -
197L TPO 4.1 11.4 + - - -
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Residues in contact with HIS 87 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83L LYS 5.0 2.4 + - - -
84L GLN* 2.7 36.3 + - + +
85L ILE 3.3 0.6 - - - -
86L GLU* 1.3 79.9 - - + +
88L THR* 1.3 60.8 + - + +
90L ASN* 3.3 19.6 + - - +
91L GLU* 2.9 27.7 + - - +
165L ARG* 3.6 10.7 + - - -
186L GLY 3.4 23.1 - - - +
187L PHE* 3.8 15.6 - + - -
197L TPO 2.6 41.3 + - + -
199L CYS* 4.6 0.4 - - - -
24N ASP* 3.3 21.8 - - - -
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Residues in contact with THR 88 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54L PHE* 4.7 6.1 - - + -
74L LEU* 3.4 33.4 - - + -
79L VAL* 4.1 11.7 - - + -
84L GLN* 3.2 16.1 + - + +
85L ILE 2.8 19.4 + - - -
87L HIS* 1.3 76.1 - - + +
89L LEU* 1.3 60.4 + - - +
91L GLU* 3.4 13.1 + - - +
92L LYS* 3.2 23.0 + - - +
116L LEU* 4.1 10.1 - - + +
118L MET* 5.1 1.1 - - - +
347L PHE* 3.7 16.8 - - - -
350L PHE* 4.0 9.1 - - - -
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Residues in contact with LEU 89 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85L ILE* 3.3 20.8 + - + +
86L GLU* 3.5 13.7 - - + +
87L HIS 3.2 0.6 - - - -
88L THR* 1.3 78.7 + - - +
90L ASN* 1.3 64.0 + - - +
92L LYS* 4.3 1.9 - - - +
93L ARG* 3.1 27.3 + - - +
346L GLU 4.3 14.6 - - - +
347L PHE* 4.5 13.7 - - + -
349L GLU* 3.5 45.2 - - + +
350L PHE* 4.0 29.6 - - + +
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Residues in contact with ASN 90 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30L TRP* 5.7 5.1 - - - -
86L GLU* 2.9 31.7 + - - +
87L HIS* 3.4 23.9 - - - +
89L LEU* 1.3 74.0 - - - +
91L GLU* 1.3 60.0 + - - +
93L ARG* 3.3 3.5 + - - +
94L ILE* 2.8 41.9 + - + +
188L ALA 3.1 25.4 + - - +
189L LYS* 3.9 26.7 - - - +
190L ARG 5.3 1.7 + - - -
197L TPO 5.0 0.2 + - - -
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Residues in contact with GLU 91 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72L LYS* 2.9 30.0 + - - +
74L LEU* 4.7 1.2 - - - +
87L HIS 2.9 12.3 + - - +
88L THR* 3.5 21.2 - - - +
89L LEU 3.3 0.2 - - - -
90L ASN* 1.3 75.4 - - - +
92L LYS* 1.3 63.1 + - - +
94L ILE* 4.0 2.0 - - - +
95L LEU* 3.0 36.0 + - + +
118L MET* 3.8 20.4 - - - +
185L PHE* 3.6 23.4 + - - +
186L GLY* 3.8 14.8 + - - -
351L G98 2.7 32.4 + - - +
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Residues in contact with LYS 92 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33L PRO* 4.6 9.9 - - - +
34L ALA 3.0 25.0 + - - +
35L GLN* 3.4 8.7 - - - +
88L THR 3.2 5.5 + - - +
89L LEU 4.3 2.7 - - - +
91L GLU* 1.3 79.2 - - - +
93L ARG* 1.3 65.9 + - - +
95L LEU* 3.9 3.4 - - - +
96L GLN* 3.1 33.4 + - + +
106L LEU* 4.4 4.9 - - + +
109L SER* 3.7 29.6 - - - +
118L MET* 4.4 12.5 - - + -
349L GLU* 3.9 6.5 + - - -
350L PHE* 3.1 66.0 + - + +
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Residues in contact with ARG 93 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30L TRP* 3.1 75.8 + - + +
31L GLU* 5.1 2.2 + - - +
33L PRO* 4.5 13.1 - - + +
89L LEU 3.1 20.4 + - - +
90L ASN* 3.3 3.8 + - - +
92L LYS* 1.3 81.7 - - - +
94L ILE* 1.3 62.5 + - - +
96L GLN* 2.8 35.0 + - - +
97L ALA* 3.6 4.5 + - - +
349L GLU* 4.1 21.2 + - - +
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Residues in contact with ILE 94 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26L PHE* 5.0 0.4 - - - -
30L TRP* 3.7 17.9 - - + -
90L ASN* 2.8 22.1 + - + +
91L GLU* 4.0 2.2 - - - +
93L ARG* 1.3 75.0 - - - +
95L LEU* 1.3 66.6 + - - +
97L ALA* 3.0 12.7 + - - +
98L VAL* 3.1 34.7 + - + +
162L LEU* 3.7 32.3 - - + -
185L PHE* 3.9 22.2 - - + -
188L ALA* 3.5 41.5 - - + +
189L LYS* 3.6 9.6 - - - +
190L ARG 4.1 0.9 - - - +
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Residues in contact with LEU 95 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91L GLU* 3.0 30.5 + - + +
92L LYS* 3.5 3.1 + - - +
94L ILE* 1.3 77.2 - - - +
96L GLN* 1.3 63.1 + - - +
97L ALA 3.2 0.9 + - - -
98L VAL* 3.2 29.9 + - + +
104L VAL 3.6 23.6 - - - +
106L LEU* 4.1 29.0 + - + +
118L MET* 4.8 4.7 - - - -
185L PHE* 4.1 21.8 - - + -
351L G98 3.3 50.3 - - + +
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Residues in contact with GLN 96 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29L LYS* 3.1 40.8 + - - +
30L TRP* 4.1 2.6 - - - +
32L ASN 4.4 0.5 - - - +
33L PRO* 3.3 33.9 - - + +
34L ALA* 3.4 17.1 + - + +
92L LYS* 3.1 31.3 + - + +
93L ARG* 2.8 24.3 + - - +
95L LEU* 1.3 79.4 - - - +
97L ALA* 1.3 66.3 + - - +
98L VAL 4.8 1.7 - - - +
106L LEU* 4.2 17.9 - - + +
109L SER* 5.7 0.4 - - - +
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Residues in contact with ALA 97 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25L ASP* 4.8 1.6 - - - +
26L PHE* 3.4 58.2 + - + +
29L LYS* 3.7 21.6 + - + +
30L TRP* 3.9 4.7 - - + +
93L ARG 3.7 3.1 - - - +
94L ILE 3.0 5.1 + - - +
96L GLN* 1.3 95.2 - - - +
98L VAL* 1.3 61.8 + - - +
99L ASN 4.1 0.3 + - - -
156L TYR* 4.8 0.7 + - - -
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Residues in contact with VAL 98 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26L PHE* 4.2 7.6 - - + -
29L LYS* 4.9 2.8 + - - -
94L ILE* 3.2 30.1 - - + +
95L LEU* 3.2 34.4 + - + +
96L GLN 4.8 1.6 - - - +
97L ALA* 1.3 80.5 - - - +
99L ASN* 1.3 63.3 + - - +
103L LEU* 4.0 23.1 - - + -
104L VAL 5.6 1.3 - - - +
105L LYS* 5.7 4.7 - - - +
156L TYR* 3.8 10.3 - - + +
157L LEU* 4.5 9.0 - - + -
162L LEU* 4.0 17.3 - - + -
185L PHE* 5.0 3.1 - - + -
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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