Contacts of the helix formed by residues 86 - 101 (chain C) in PDB entry 3NT7
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 LYS 86 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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70C TYR* 3.5 53.3 - - + +
72C LYS* 3.2 28.4 + - - +
73C ASP* 2.9 35.3 + - - -
81C SER* 3.3 19.1 + - - +
83C ASN* 6.0 0.2 - - - -
85C THR* 1.3 83.4 + - - +
87C LYS* 1.3 66.2 + - - +
88C SER 3.2 1.0 + - - -
89C ILE* 3.4 2.9 + - - +
90C LYS* 3.2 22.2 + - - +
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Residues in contact with LYS 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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85C THR 3.4 5.2 + - - -
86C LYS* 1.3 72.6 - - - +
88C SER* 1.3 57.7 + - - +
90C LYS* 3.5 23.0 + - + +
91C GLU* 3.0 63.6 + - - +
183C ALA* 4.2 21.1 - - + +
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Residues in contact with SER 88 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70C TYR* 3.8 23.0 - - - -
79C PHE* 4.5 9.6 - - - -
86C LYS* 3.2 1.6 + - - +
87C LYS* 1.3 78.3 - - - +
89C ILE* 1.3 58.6 + - - +
91C GLU 3.2 1.6 + - - -
92C ILE* 2.9 33.3 + - - +
181C HIS* 3.4 27.5 + - - -
182C PRO* 3.6 23.5 - - - +
183C ALA* 4.6 3.1 - - - +
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Residues in contact with ILE 89 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70C TYR* 3.5 4.9 + - - +
79C PHE* 3.3 43.5 - - + +
81C SER* 3.7 22.2 - - - +
84C PHE* 3.8 14.5 - - + -
86C LYS 3.4 11.6 + - - +
88C SER* 1.3 75.3 - - - +
90C LYS* 1.3 63.9 + - - +
92C ILE* 3.8 9.2 - - + +
93C ALA* 2.9 27.9 + - - +
108C TYR* 3.1 47.3 - - + +
109C ASN* 4.6 0.2 - - - -
110C LEU* 4.4 14.8 - - + +
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Residues in contact with LYS 90 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84C PHE* 3.8 44.8 + - + +
85C THR* 3.6 29.3 + - - +
86C LYS 3.2 10.2 + - - +
87C LYS* 3.6 25.4 - - + +
89C ILE* 1.3 78.1 - - - +
91C GLU* 1.3 57.4 + - - +
93C ALA* 3.3 3.6 + - - +
94C SER* 3.0 30.5 + - - -
105C TYR* 4.8 0.7 + - - -
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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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87C LYS* 3.0 53.6 + - - +
88C SER 3.7 4.0 - - - +
90C LYS* 1.3 73.3 - - - +
92C ILE* 1.3 64.5 + - - +
94C SER* 3.4 12.9 + - - -
95C SER* 3.1 25.3 + - - -
98C ARG* 4.6 6.8 + - - -
182C PRO* 3.3 28.5 - - + +
183C ALA* 4.5 4.0 - - - -
188C GLN* 5.7 2.9 + - - +
191C LYS* 3.9 16.1 + - - +
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Residues in contact with ILE 92 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79C PHE* 3.9 28.9 - - + -
88C SER 2.9 22.5 + - - +
89C ILE* 3.8 8.5 - - + +
90C LYS 3.4 0.2 - - - -
91C GLU* 1.3 76.0 - - - +
93C ALA* 1.3 61.7 + - - +
95C SER* 3.3 3.5 + - - -
96C ILE* 3.1 24.3 + - + +
108C TYR* 3.8 25.6 - - + -
110C LEU* 4.1 19.5 - - + -
158C LEU* 4.7 6.5 - - + -
182C PRO* 4.0 20.9 - - + -
195C PHE* 3.7 33.7 - - + -
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Residues in contact with ALA 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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84C PHE* 3.7 15.5 - - + -
89C ILE 2.9 18.3 + - - +
90C LYS 3.5 6.1 - - - +
91C GLU 3.3 0.2 - - - -
92C ILE* 1.3 75.6 - - - +
94C SER* 1.3 58.1 + - - +
96C ILE* 3.4 1.5 + - - +
97C SER* 2.9 28.8 + - - -
105C TYR* 3.7 14.7 + - + -
108C TYR* 3.5 34.1 - - + -
216C PHE* 3.8 5.4 - - - -
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Residues in contact with SER 94 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90C LYS 3.0 16.3 + - - -
91C GLU* 3.5 18.3 + - - -
92C ILE 3.3 0.2 - - - -
93C ALA* 1.3 73.8 - - - +
95C SER* 1.3 64.9 + - - +
97C SER* 3.2 6.1 + - - -
98C ARG* 3.0 49.1 + - - +
105C TYR* 3.8 12.1 + - - -
220C SO4 4.4 5.0 + - - -
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Residues in contact with SER 95 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91C GLU 3.1 11.3 + - - -
92C ILE* 3.3 9.1 + - - -
94C SER* 1.3 77.7 - - - +
96C ILE* 1.3 59.3 + - - +
98C ARG* 3.2 8.9 + - - +
99C LEU* 2.9 32.3 + - - +
191C LYS* 4.2 12.3 - - - +
192C ASP* 2.6 36.1 + - - +
195C PHE* 4.0 22.6 - - - -
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Residues in contact with ILE 96 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92C ILE* 3.1 21.5 + - + +
93C ALA 3.9 4.0 - - - +
95C SER* 1.3 73.7 - - - +
97C SER* 1.3 53.7 + - - +
99C LEU* 3.3 8.2 + - + -
100C THR* 2.5 44.5 + - + +
108C TYR* 3.4 28.7 - - + +
195C PHE* 3.9 33.7 - - + -
212C TRP* 3.8 38.8 - - + +
216C PHE* 3.6 23.8 - - + -
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Residues in contact with SER 97 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93C ALA 2.9 14.7 + - - -
94C SER* 3.4 11.0 - - - -
96C ILE* 1.3 76.8 - - - +
98C ARG* 1.3 58.0 + - - +
100C THR* 3.8 2.7 - - - -
101C GLY* 2.8 31.0 + - - -
102C VAL 2.7 27.5 + - - -
103C ILE* 3.9 14.2 - - - +
105C TYR* 4.1 16.0 - - - -
216C PHE* 3.7 3.3 - - - -
220C SO4 4.9 7.4 + - - -
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Residues in contact with ARG 98 (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* 4.6 8.3 + - - -
94C SER* 3.0 30.7 + - - +
95C SER* 3.6 19.7 + - - +
97C SER* 1.3 78.2 - - - +
99C LEU* 1.3 60.9 + - - +
100C THR 3.6 0.3 + - - -
101C GLY* 4.5 2.3 + - - -
188C GLN* 3.4 37.8 + - - +
191C LYS* 5.8 1.6 - - - +
192C ASP* 2.8 43.2 + - + +
220C SO4 2.9 44.7 + - - +
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Residues in contact with LEU 99 (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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95C SER 2.9 17.5 + - - +
96C ILE* 3.3 14.6 + - + +
98C ARG* 1.3 78.3 - - - +
100C THR* 1.3 62.9 + - + +
192C ASP* 3.2 36.8 - - + +
193C ARG* 4.5 8.1 - - - +
195C PHE* 3.5 23.3 - - + -
196C GLU* 3.7 40.4 - - + +
212C TRP* 5.6 3.6 - - + -
221C GOL 4.4 22.3 - - - +
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Residues in contact with THR 100 (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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96C ILE* 2.5 38.3 + - + +
99C LEU* 1.3 85.1 - - + +
101C GLY* 1.3 61.4 + - - +
102C VAL* 3.5 19.3 + - - +
212C TRP* 5.0 5.2 - - + +
213C ALA* 4.5 18.4 - - + +
216C PHE* 3.8 10.4 - - - -
221C GOL 5.4 9.0 - - - +
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Residues in contact with GLY 101 (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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97C SER 2.8 16.7 + - - -
98C ARG 4.5 2.5 + - - -
100C THR* 1.3 74.5 - - - +
102C VAL* 1.3 62.5 + - - +
103C ILE* 3.5 15.7 + - - +
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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