Contacts of the helix formed by residues 58 - 70 (chain H) in PDB entry 1JJ2
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 HIS 58 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24H PRO* 5.3 3.9 - - + +
25H GLY 3.4 12.7 + - - -
26H LYS* 3.3 24.7 - - + -
27H LYS* 2.8 53.6 - - + +
28H ILE* 3.8 4.0 - - + +
56H ILE 3.6 1.0 + - - -
57H ARG* 1.3 70.5 - - - +
59H ASN* 1.3 88.5 + - - +
61H LEU* 3.5 14.4 - - - -
62H GLU* 3.2 23.7 + - - +
89H PRO* 4.0 7.4 - - + -
93H ILE* 6.4 0.2 - - + -
119H VAL 5.4 1.1 - - - -
120H GLY* 4.5 8.5 - - - -
121H THR* 3.0 44.6 + - - +
122H ALA* 4.3 0.2 - - - +
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Residues in contact with ASN 59 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25190 C 3.9 32.4 + - - +
25200 G 4.6 1.6 - - - +
27H LYS* 3.6 27.6 + - - +
57H ARG* 2.8 36.7 + - + +
58H HIS* 1.3 107.4 + - - +
60H ALA* 1.3 62.3 + - - +
62H GLU* 3.7 2.9 - - - +
63H ALA* 3.2 21.8 + - - +
93H ILE* 6.2 0.2 - - - +
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Residues in contact with ALA 60 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25190 C 3.6 20.1 + - - +
25200 G 3.9 12.3 - - - +
56H ILE* 3.8 15.5 - - + -
57H ARG* 2.8 11.6 + - - +
59H ASN* 1.3 76.8 - - - +
61H LEU* 1.3 61.5 + - - +
63H ALA* 3.8 0.3 - - - +
64H ALA* 2.8 34.5 + - - +
152H LYS 3.5 18.5 - - - +
153H VAL* 4.3 3.4 - - + -
154H THR 5.6 0.2 - - - +
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Residues in contact with LEU 61 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28H ILE* 3.4 29.2 - - + -
56H ILE* 3.0 38.6 - - + +
57H ARG 3.0 32.7 + - - +
58H HIS* 3.5 7.2 - - - +
60H ALA* 1.3 77.8 - - - +
62H GLU* 1.3 53.1 + - - +
64H ALA* 3.6 4.2 - - + +
65H ARG* 2.7 38.3 + - - +
85H ILE* 4.3 13.9 - - + -
87H LYS* 5.5 3.4 - - + +
89H PRO* 4.8 2.2 - - + -
123H ALA* 4.4 15.9 - - + +
125H VAL* 6.2 0.4 - - + -
131H ILE* 3.6 26.9 - - + -
132H PHE* 4.6 2.6 - - + -
153H VAL* 5.2 1.1 - - + -
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Residues in contact with GLU 62 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27H LYS* 2.8 30.5 - - + +
28H ILE* 2.8 9.4 - - - +
29H ALA* 2.6 33.7 + - - +
58H HIS 3.2 15.3 + - - +
59H ASN 3.7 3.6 - - - +
61H LEU* 1.3 80.1 - - - +
63H ALA* 1.3 57.2 + - - +
65H ARG* 3.2 18.2 + - - -
66H VAL* 2.7 63.2 + - + +
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Residues in contact with ALA 63 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25180 C 4.1 14.6 - - - +
25190 C 3.3 42.0 - - - +
59H ASN 3.2 6.3 + - - +
60H ALA 4.0 2.0 - - - +
62H GLU* 1.3 79.9 - - - +
64H ALA* 1.3 58.3 + - - +
66H VAL* 4.0 4.4 - - - +
67H ALA* 3.0 31.9 + - - +
70H ARG* 5.6 0.2 + - - -
152H LYS* 3.7 12.8 + - + +
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Residues in contact with ALA 64 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60H ALA 2.8 23.9 + - - +
61H LEU* 3.6 4.0 - - - +
63H ALA* 1.3 73.0 - - - +
65H ARG* 1.3 63.5 + - - +
67H ALA* 3.6 1.7 + - - +
68H ALA* 3.2 23.0 + - - +
132H PHE* 4.2 15.7 - - + -
149H ALA* 3.7 30.4 - - - +
152H LYS* 4.2 7.1 - - + +
153H VAL* 3.8 16.4 - - + -
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Residues in contact with ARG 65 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28H ILE* 4.8 2.9 - - + -
29H ALA* 3.1 21.2 - - - +
30H GLN* 2.9 65.5 + - - +
33H MET* 3.4 36.1 - - + -
61H LEU 2.7 23.1 + - - +
62H GLU* 3.2 23.6 + - - +
64H ALA* 1.3 72.3 - - - +
66H VAL* 1.3 81.0 + - - +
68H ALA* 3.0 4.5 + - - +
69H ASN* 2.8 29.1 + - - +
83H PHE* 4.4 0.6 - - + -
85H ILE* 4.4 6.3 - - + -
132H PHE* 3.7 23.1 - - + -
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Residues in contact with VAL 66 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62H GLU* 2.7 52.2 + - + +
63H ALA* 4.0 4.3 - - - +
65H ARG* 1.3 86.7 - - - +
67H ALA* 1.3 57.1 + - - +
68H ALA 3.0 0.2 + - - -
69H ASN* 4.9 0.7 - - - -
70H ARG* 2.6 76.1 + - + +
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Residues in contact with ALA 67 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25020 C 6.0 0.4 - - - +
63H ALA 3.0 20.3 + - - +
64H ALA 3.9 3.8 - - - +
66H VAL* 1.3 77.0 - - - +
68H ALA* 1.3 59.3 + - - +
70H ARG* 4.2 14.9 + - - +
71H TYR* 3.4 18.6 + - - +
145H ALA 4.6 1.8 - - - -
148H ARG* 4.1 28.6 + - + +
152H LYS* 3.7 27.6 - - + +
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Residues in contact with ALA 68 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64H ALA 3.2 16.2 + - - +
65H ARG* 3.0 5.3 + - - +
67H ALA* 1.3 77.5 - - - +
69H ASN* 1.3 60.2 + - - +
71H TYR* 3.3 2.1 + - - +
72H VAL* 2.9 22.1 + - - +
83H PHE* 3.6 26.0 - - + -
132H PHE* 5.5 0.9 - - + -
145H ALA* 3.2 38.5 - - + +
149H ALA* 4.0 8.5 - - + -
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Residues in contact with ASN 69 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30H GLN* 5.0 6.8 + - - +
33H MET* 3.6 43.8 - - - +
65H ARG* 2.8 24.0 + - - +
66H VAL* 4.3 1.3 - - - +
68H ALA* 1.3 70.1 - - - +
70H ARG* 1.3 61.7 + - - +
71H TYR 2.9 4.9 - - - -
72H VAL* 2.9 29.8 + - - +
73H GLN* 3.1 17.4 + - - -
81H TYR* 3.0 28.8 + - - -
83H PHE* 3.9 6.9 - - + -
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Residues in contact with ARG 70 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25030 A 6.4 0.2 - - - -
25040 A 3.2 63.7 + - - -
25050 G 5.6 0.2 - - - -
25170 A 4.8 10.3 + - - -
25180 C 5.4 1.2 + - - -
63H ALA 5.6 0.2 + - - -
66H VAL* 2.6 57.4 + - + +
67H ALA* 4.2 18.5 + - - +
69H ASN* 1.3 73.3 + - - +
71H TYR* 1.3 56.8 + - - +
73H GLN* 3.5 22.5 - - - +
148H ARG* 5.8 0.6 - - - +
152H LYS* 4.8 10.3 - - - +
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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
------------------------------------------------------------
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