Contacts of the helix formed by residues 84 - 96 (chain F) in PDB entry 3E8C
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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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54F PHE* 3.9 35.1 - - + -
79F VAL* 2.8 22.6 + - + +
82F LEU* 2.9 30.4 + - + +
83F LYS* 1.3 81.2 + - - +
85F ILE* 1.3 59.5 + - - +
86F GLU 3.5 2.2 - - - -
87F HIS* 2.8 36.2 + - + +
88F THR* 2.8 32.3 + - - +
187F PHE* 3.7 17.3 - - - -
23L HIS* 5.0 12.5 - - - +
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Residues in contact with ILE 85 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79F VAL* 3.6 7.6 - - - +
80F VAL* 3.8 47.1 - - + +
83F LYS* 3.5 4.0 - - - -
84F GLN* 1.3 78.9 - - - +
86F GLU* 1.3 65.0 + - - +
88F THR* 3.2 3.8 + - - -
89F LEU* 3.1 31.1 + - + +
346F GLU* 3.8 37.5 - - + +
347F PHE* 4.1 13.0 - - + -
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Residues in contact with GLU 86 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85F ILE* 1.3 81.3 - - - +
87F HIS* 1.3 61.9 + - + +
89F LEU* 3.2 18.2 + - - +
90F ASN* 2.8 51.4 + - - +
189F LYS* 5.4 7.6 - - - -
197F TPO 5.7 3.6 - - - +
349F GLU* 5.5 0.7 - - - +
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Residues in contact with HIS 87 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83F LYS 4.5 4.2 + - - -
84F GLN* 2.8 42.6 + - + +
85F ILE 3.3 0.4 - - - -
86F GLU* 1.3 80.5 - - + +
88F THR* 1.3 55.3 + - - +
90F ASN* 3.4 13.4 + - - +
91F GLU* 2.9 30.5 + - - +
165F ARG* 3.7 15.0 + - - -
186F GLY 3.3 23.5 - - - +
187F PHE* 4.0 14.8 - + - -
197F TPO 2.8 48.4 + - + +
199F CYS* 4.5 3.6 - - + -
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Residues in contact with THR 88 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54F PHE* 4.5 6.8 - - - -
74F LEU* 4.9 4.8 - - + +
79F VAL* 3.4 19.7 - - - +
84F GLN* 2.8 22.5 + - - +
85F ILE 3.5 8.7 - - - -
87F HIS* 1.3 73.6 - - - +
89F LEU* 1.3 62.6 + - + +
91F GLU* 3.5 11.6 + - - +
92F LYS* 3.2 22.5 + - - +
116F LEU* 3.3 32.5 - - + -
118F MET* 4.7 9.7 - - + +
347F PHE* 4.7 3.1 - - + -
350F PHE* 4.1 12.9 - - + -
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Residues in contact with LEU 89 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85F ILE* 3.1 24.6 + - + +
86F GLU* 3.6 20.2 - - - +
88F THR* 1.3 72.6 - - - +
90F ASN* 1.3 66.3 + - - +
92F LYS* 3.5 4.1 + - - +
93F ARG* 3.1 27.9 + - - +
346F GLU 4.1 15.5 - - - +
347F PHE* 4.7 12.6 - - + -
349F GLU* 3.8 44.8 - - + +
350F PHE* 3.9 31.4 - - + +
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Residues in contact with ASN 90 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30F TRP* 5.6 5.8 - - - -
86F GLU* 2.8 46.5 + - - +
87F HIS* 3.5 14.2 - - - +
89F LEU* 1.3 76.3 - - - +
91F GLU* 1.3 57.6 + - - +
93F ARG* 3.9 3.5 - - - +
94F ILE* 2.9 42.9 + - + +
188F ALA 3.2 19.5 + - - +
189F LYS* 3.7 31.2 - - - +
190F ARG 5.3 1.2 + - - -
197F TPO 5.2 0.2 + - - -
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Residues in contact with GLU 91 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54F PHE* 6.1 0.5 - - - -
72F LYS* 2.9 29.6 + - - -
74F LEU* 5.6 0.5 - - - +
87F HIS 2.9 15.6 + - - +
88F THR* 3.6 12.3 + - - +
89F LEU 3.3 0.2 - - - -
90F ASN* 1.3 75.8 - - - +
92F LYS* 1.3 57.4 + - - +
94F ILE* 4.1 2.5 - - - +
95F LEU* 3.0 40.9 + - + +
118F MET* 3.4 23.6 - - + +
185F PHE* 3.3 23.9 + - - +
186F GLY* 3.3 20.4 + - - -
188F ALA 5.1 0.2 - - - -
351F G96 2.7 28.1 + - - +
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Residues in contact with LYS 92 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33F PRO* 5.2 6.7 - - - +
34F ALA 3.0 24.9 + - - +
35F GLN* 3.7 5.9 - - - +
88F THR 3.2 7.1 + - - +
89F LEU* 4.1 3.6 - - - +
91F GLU* 1.3 76.9 - - - +
93F ARG* 1.3 68.9 + - - +
95F LEU* 3.4 3.4 + - - +
96F GLN* 3.1 31.1 + - + +
106F LEU* 4.1 7.0 - - + +
109F SER* 3.8 21.8 + - - +
118F MET* 4.1 14.3 - - - -
349F GLU 4.0 5.1 + - - -
350F PHE* 2.7 76.3 + - + +
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Residues in contact with ARG 93 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30E TRP* 6.1 1.2 - - - +
30F TRP* 3.3 72.1 + - + +
31F GLU* 5.5 1.2 - - - +
33F PRO* 4.9 12.9 - - + +
89F LEU 3.1 18.5 + - - +
90F ASN* 4.0 2.5 - - - +
92F LYS* 1.3 83.3 - - - +
94F ILE* 1.3 62.5 + - - +
96F GLN* 2.9 36.5 + - - +
97F ALA* 3.6 4.5 - - - +
349F GLU* 4.9 15.4 + - - +
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Residues in contact with ILE 94 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26F PHE* 5.0 0.2 - - - -
30F TRP* 3.6 24.5 - - + -
90F ASN* 2.9 21.0 + - + +
91F GLU 4.1 2.0 - - - +
93F ARG* 1.3 73.7 - - - +
95F LEU* 1.3 65.9 + - - +
97F ALA* 3.0 13.0 + - - +
98F VAL* 3.1 18.8 + - + +
162F LEU* 3.8 37.5 - - + -
185F PHE* 3.9 22.7 - - + -
188F ALA* 3.5 40.2 - - + +
189F LYS* 3.6 10.8 - - - +
190F ARG 3.9 2.9 - - - +
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Residues in contact with LEU 95 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91F GLU* 3.0 29.1 + - + +
92F LYS 3.4 3.8 + - - +
94F ILE* 1.3 77.6 - - - +
96F GLN* 1.3 59.3 + - - +
97F ALA 3.4 0.9 + - - -
98F VAL* 3.4 24.7 + - + +
104F VAL 3.9 22.2 - - - +
105F LYS* 5.9 0.2 - - - -
106F LEU* 4.0 29.3 + - + +
118F MET* 4.5 6.1 - - - -
185F PHE* 4.0 31.4 - - + -
351F G96 3.2 46.7 - - + +
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Residues in contact with GLN 96 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29F LYS* 2.9 40.5 + - - +
30F TRP* 4.1 4.0 - - - +
32F ASN 4.5 0.7 - - - +
33F PRO* 3.3 34.3 - - + +
34F ALA* 3.4 17.6 + - + +
92F LYS* 3.1 26.7 + - + +
93F ARG* 2.9 24.9 + - - +
95F LEU* 1.3 75.6 - - - +
97F ALA* 1.3 65.9 + - - +
98F VAL 4.8 1.2 - - - +
106F LEU* 4.1 17.2 - - + +
109F SER* 6.0 0.2 - - - +
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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