Contacts of the helix formed by residues 84 - 97 (chain C) in PDB entry 1J7H
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 ASP 84 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47C ILE* 3.3 47.3 - - + +
81C ASP* 2.7 31.7 + - + +
83C ASN* 1.3 78.8 - - - +
85C PHE* 1.3 61.4 + - - +
86C ALA 2.9 7.4 + - - -
87C ALA* 2.9 20.5 + - - +
88C VAL* 3.3 12.7 + - + +
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Residues in contact with PHE 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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116A PRO* 6.3 3.6 - - + -
77C VAL* 5.2 3.1 - - + -
79C VAL* 3.6 28.2 - - + +
81C ASP 3.5 3.4 + - - +
82C LEU* 3.3 29.4 + - + +
83C ASN 3.3 0.4 - - - -
84C ASP* 1.3 77.2 - - - +
86C ALA* 1.3 55.2 + - - +
88C VAL* 3.6 19.5 - - + +
89C ASN* 2.6 66.6 + - + +
107C ARG* 3.1 32.8 - - - -
109C CYS* 3.9 27.1 - - + -
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Residues in contact with ALA 86 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82C LEU 4.4 0.8 + - - -
83C ASN 3.8 15.3 + - - +
84C ASP 2.9 0.2 + - - -
85C PHE* 1.3 80.1 - - - +
87C ALA* 1.3 56.8 + - - +
89C ASN* 4.6 2.5 - - - +
90C ALA* 3.3 23.4 + - - +
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Residues in contact with ALA 87 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47C ILE* 5.3 1.6 - - + -
48C VAL* 4.5 24.6 - - + +
84C ASP* 2.9 13.4 + - - +
86C ALA* 1.3 77.9 - - - +
88C VAL* 1.3 67.5 + - + +
89C ASN 3.4 0.2 - - - -
90C ALA* 3.6 4.6 + - - +
91C GLU* 3.1 25.1 + - - +
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Residues in contact with VAL 88 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47C ILE* 3.8 24.0 - - + +
48C VAL* 5.9 0.7 - - - +
51C ALA* 4.1 26.0 - - + +
55C LEU* 6.2 2.2 - - + -
77C VAL* 5.9 6.5 - - + -
79C VAL* 5.8 4.9 - - + -
84C ASP* 3.5 17.3 - - + +
85C PHE* 3.2 21.5 + - + +
87C ALA* 1.3 75.6 - - - +
89C ASN* 1.3 54.0 + - - +
91C GLU* 3.6 3.3 - - - +
92C TYR* 2.6 47.3 + - + +
107C ARG* 5.6 0.9 - - - +
121C LEU* 5.7 4.5 - - + -
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Residues in contact with ASN 89 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A GLY* 5.4 1.8 - - - -
17A PRO* 3.9 24.7 - - - +
85C PHE* 2.6 55.0 + - + +
86C ALA* 4.6 2.2 - - - +
88C VAL* 1.3 71.2 - - - +
90C ALA* 1.3 65.5 + - - +
92C TYR* 3.8 5.8 - - - +
93C GLU* 3.1 23.8 + - - +
107C ARG* 3.8 7.7 + - - +
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Residues in contact with ALA 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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86C ALA 3.3 19.4 + - - +
87C ALA* 3.9 6.1 - - - +
88C VAL 3.3 0.4 - - - -
89C ASN* 1.3 83.6 - - - +
91C GLU* 1.3 56.2 + - - +
93C GLU* 4.7 2.1 - - - +
94C ARG* 3.1 26.9 + - - +
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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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48C VAL* 5.0 16.6 - - + +
51C ALA* 5.4 2.8 - - + +
52C ARG* 3.7 32.0 + - - +
55C LEU* 4.5 10.9 - - - +
87C ALA 3.1 18.0 + - - +
88C VAL* 4.1 3.4 - - - +
90C ALA* 1.3 76.5 - - - +
92C TYR* 1.3 65.1 + - - +
93C GLU 3.4 0.4 - - - -
94C ARG* 3.8 7.0 - - + +
95C PHE* 3.1 31.2 + - - +
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Residues in contact with TYR 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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17A PRO* 3.3 36.5 + - + -
55C LEU* 3.8 24.2 - - + -
75C THR* 3.1 34.0 + - + +
77C VAL* 5.2 3.8 - - + -
88C VAL* 2.6 33.6 + - + +
89C ASN* 3.8 4.9 - - - +
91C GLU* 1.3 74.9 + - - +
93C GLU* 1.3 58.1 + - - +
95C PHE* 2.9 34.3 - + - -
96C PHE* 3.1 48.3 - + - -
105C PRO* 5.1 1.0 + - - +
107C ARG* 3.1 42.6 - - - +
123C ILE* 6.2 0.7 - - + -
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Residues in contact with GLU 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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15A ILE 5.8 0.2 - - - -
16A GLY* 3.5 10.1 - - - +
17A PRO* 3.4 43.1 - - + -
89C ASN* 3.1 17.1 + - - +
90C ALA* 4.7 2.6 - - - +
92C TYR* 1.3 74.8 - - - +
94C ARG* 1.3 74.1 + - - +
95C PHE 3.2 3.4 + - - -
96C PHE* 3.5 3.4 + - - +
97C LYS* 3.5 26.0 + - - +
104C PHE* 3.6 20.2 - - + -
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Residues in contact with ARG 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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90C ALA 3.1 21.8 + - - +
91C GLU* 4.0 9.0 - - + +
92C TYR 3.4 0.2 - - - -
93C GLU* 1.3 87.2 + - - +
95C PHE* 1.3 57.2 + - - +
97C LYS* 5.0 2.1 - - - +
98C GLU* 2.8 54.6 + - - +
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Residues in contact with PHE 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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52C ARG* 5.5 11.0 - - - +
55C LEU* 3.2 50.5 - - + -
59C LYS* 5.8 4.9 - - + -
69C ALA* 4.5 6.3 - - + -
72C ILE* 6.0 0.2 - - + -
91C GLU* 3.1 23.0 + - - +
92C TYR* 2.9 20.9 - + - -
94C ARG* 1.3 79.1 - - - +
96C PHE* 1.3 91.7 + + - +
97C LYS 3.4 0.4 - - - -
98C GLU* 3.9 5.8 - - - -
99C ASN* 2.6 57.0 + - - +
101C HIS* 3.8 20.0 - + - -
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Residues in contact with PHE 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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17A PRO* 5.2 2.9 - - + -
55C LEU* 4.7 0.7 - - + -
69C ALA 4.1 7.4 - - - -
72C ILE* 4.1 15.5 - - + -
92C TYR* 3.1 47.5 + + - +
93C GLU* 3.9 10.1 - - - +
95C PHE* 1.3 126.7 - + - +
97C LYS* 1.3 54.7 + - - +
99C ASN 2.8 2.6 + - - -
100C ASN 2.8 11.1 + - - -
101C HIS* 2.5 71.1 + - + +
104C PHE* 5.1 6.3 - + + -
105C PRO* 3.3 35.2 - - + -
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Residues in contact with LYS 97 (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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93C GLU* 3.5 22.3 + - - +
94C ARG* 5.0 2.0 - - - +
95C PHE 3.4 0.2 - - - -
96C PHE* 1.3 79.6 - - - +
98C GLU* 1.3 61.2 + - + +
99C ASN 3.3 0.5 + - - -
100C ASN* 3.3 9.6 + - - +
101C HIS 4.1 8.2 + - - +
102C PRO* 4.1 26.5 - - + -
104C PHE* 5.6 4.3 - - + -
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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