Contacts of the helix formed by residues 84 - 96 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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54C PHE* 4.1 31.0 - - + -
79C VAL* 2.8 23.0 + - + +
82C LEU* 3.3 27.8 + - + +
83C LYS* 1.3 82.3 + - - +
85C ILE* 1.3 58.5 + - - +
86C GLU 3.5 2.0 - - - -
87C HIS* 2.8 39.1 + - + +
88C THR* 2.8 35.2 + - - +
186C GLY 5.0 0.2 - - - +
187C PHE* 3.6 17.8 - - - -
22I ILE 5.8 0.2 + - - -
23I HIS* 4.5 15.9 - - + +
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Residues in contact with ILE 85 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79C VAL* 3.5 7.8 - - - +
80C VAL* 3.7 43.7 - - + +
83C LYS* 3.5 3.7 - - - -
84C GLN* 1.3 78.0 - - - +
86C GLU* 1.3 64.3 + - - +
88C THR* 3.2 3.3 + - - -
89C LEU* 3.1 30.9 + - + +
346C GLU* 3.7 42.0 - - + +
347C PHE* 3.9 15.8 - - + -
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Residues in contact with GLU 86 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83C LYS 5.5 0.4 + - - -
85C ILE* 1.3 80.0 - - - +
87C HIS* 1.3 61.5 + - + +
89C LEU* 3.3 12.0 + - + +
90C ASN* 2.8 48.2 + - - +
189C LYS* 4.0 15.8 + - - -
197C TPO 3.7 20.5 + - - -
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Residues in contact with HIS 87 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83C LYS 4.7 3.7 + - - -
84C GLN* 2.8 43.7 + - + +
85C ILE 3.2 0.4 - - - -
86C GLU* 1.3 81.6 - - + +
88C THR* 1.3 56.9 + - - +
90C ASN* 3.4 14.2 + - - +
91C GLU* 2.9 30.4 + - - +
165C ARG* 3.7 12.7 + - - -
186C GLY 3.3 23.4 - - - +
187C PHE* 3.9 17.4 - + - -
197C TPO 2.7 48.9 + - + +
199C CYS* 4.3 4.0 - - + -
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Residues in contact with THR 88 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54C PHE* 4.6 7.1 - - - -
74C LEU* 4.8 3.8 - - + +
79C VAL* 3.8 19.6 - - - +
84C GLN* 2.8 24.3 + - - +
85C ILE 3.6 4.7 - - - -
87C HIS* 1.3 73.2 - - - +
89C LEU* 1.3 61.6 + - - +
91C GLU* 3.5 13.4 + - - +
92C LYS* 3.2 22.2 + - - +
116C LEU* 3.3 32.5 - - + -
118C MET* 4.9 9.4 - - + +
347C PHE* 4.6 3.8 - - + -
350C PHE* 4.0 14.7 - - + -
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Residues in contact with LEU 89 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85C ILE* 3.1 34.1 + - + +
86C GLU* 3.6 10.5 - - + +
88C THR* 1.3 74.9 - - - +
90C ASN* 1.3 65.7 + - - +
92C LYS* 3.5 4.8 + - - +
93C ARG* 3.1 27.6 + - - +
346C GLU 4.2 9.9 - - - +
347C PHE* 4.7 12.6 - - + -
349C GLU* 4.6 15.3 - - + +
350C PHE* 4.1 39.0 - - + +
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Residues in contact with ASN 90 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30C TRP* 5.9 3.4 - - - -
86C GLU* 2.8 43.6 + - - +
87C HIS* 3.5 17.5 - - - +
89C LEU* 1.3 76.8 - - - +
91C GLU* 1.3 56.9 + - - +
93C ARG* 3.8 3.5 - - - +
94C ILE* 2.9 44.3 + - + +
188C ALA 3.2 23.3 + - - +
189C LYS* 4.1 22.3 - - - +
190C ARG 5.4 0.9 + - - -
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Residues in contact with GLU 91 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54C PHE* 6.0 1.2 - - - -
72C LYS* 2.6 28.0 + - - -
74C LEU* 5.5 0.3 - - - +
87C HIS 2.9 15.1 + - - +
88C THR* 3.5 14.6 + - - +
89C LEU 3.3 0.2 - - - -
90C ASN* 1.3 76.8 - - - +
92C LYS* 1.3 56.7 + - - +
94C ILE* 4.1 2.4 - - - +
95C LEU* 3.0 42.6 + - + +
118C MET* 3.2 23.7 - - + +
185C PHE* 3.3 26.6 + - - +
186C GLY* 3.6 15.5 + - - -
351C G96 2.5 27.7 + - - +
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Residues in contact with LYS 92 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33C PRO* 4.9 8.7 - - - +
34C ALA 3.1 22.4 + - - +
35C GLN* 3.7 8.1 - - - +
88C THR 3.2 13.4 + - - +
89C LEU* 4.0 4.0 - - - +
91C GLU* 1.3 77.2 - - - +
93C ARG* 1.3 70.6 + - - +
95C LEU* 3.5 3.8 + - - +
96C GLN* 3.2 31.0 + - + +
106C LEU* 3.9 6.1 - - + +
109C SER* 3.8 22.8 + - - +
118C MET* 4.2 13.7 - - - -
349C GLU 3.9 6.6 + - - -
350C PHE* 3.1 64.2 + - + +
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Residues in contact with ARG 93 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30C TRP* 3.4 73.5 + - + +
31C GLU* 5.2 2.0 + - - +
33C PRO* 4.9 10.4 - - + +
89C LEU 3.1 18.9 + - - +
90C ASN* 4.0 3.6 - - - +
92C LYS* 1.3 82.0 - - - +
94C ILE* 1.3 63.0 + - - +
96C GLN* 2.9 36.5 + - - +
97C ALA* 3.6 5.7 + - - +
190D ARG* 6.2 0.2 - - - +
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Residues in contact with ILE 94 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26C PHE* 5.2 0.7 - - + -
30C TRP* 3.8 24.0 - - + -
90C ASN* 2.9 25.5 + - + +
91C GLU 4.1 2.0 - - - +
93C ARG* 1.3 74.8 - - - +
95C LEU* 1.3 66.9 - - - +
97C ALA* 3.0 12.5 + - - +
98C VAL* 3.1 19.1 + - + +
162C LEU* 3.9 32.5 - - + -
185C PHE* 3.9 22.2 - - + -
188C ALA* 3.4 39.3 - - + +
189C LYS* 3.7 9.9 - - - +
190C ARG 4.1 6.5 - - - +
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Residues in contact with LEU 95 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91C GLU* 3.0 31.6 + - + +
92C LYS 3.5 0.4 + - - +
94C ILE* 1.3 76.9 - - - +
96C GLN* 1.3 60.4 + - - +
97C ALA 3.3 0.9 + - - -
98C VAL* 3.4 25.2 + - + +
103C LEU* 6.4 0.2 - - + -
104C VAL 3.9 18.6 - - - +
105C LYS* 5.9 0.2 - - - -
106C LEU* 3.7 34.2 + - + +
118C MET* 4.3 6.7 - - - -
185C PHE* 4.1 25.8 - - + -
351C G96 3.3 52.5 - - + +
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Residues in contact with GLN 96 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29C LYS* 3.1 37.0 + - - +
30C TRP* 4.3 1.4 - - - +
32C ASN 4.4 0.7 - - - +
33C PRO* 3.2 35.7 - - + +
34C ALA* 3.3 18.0 + - + +
92C LYS* 3.2 24.5 + - + +
93C ARG* 2.9 27.1 + - - +
95C LEU* 1.3 77.7 - - - +
97C ALA* 1.3 65.8 + - - +
98C VAL 4.8 1.6 - - - +
106C LEU* 4.0 16.5 - - + +
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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