Contacts of the helix formed by residues 46 - 66 (chain B) 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 46 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44B PRO* 3.1 3.2 - - + -
45B ALA* 1.3 74.8 - - - +
47B ILE* 1.3 56.9 + - - +
48B VAL* 2.9 10.5 - - - +
49B ALA* 2.6 49.9 + - + +
50B GLN* 2.7 15.1 + - - -
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Residues in contact with ILE 47 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45B ALA 2.7 13.9 + - - +
46B ASP* 1.3 70.3 - - - +
48B VAL* 1.3 55.0 + - + +
50B GLN* 3.2 26.7 - - + +
51B ALA* 2.8 37.1 + - - +
81B ASP* 6.0 2.2 - - + -
84B ASP* 3.3 49.1 - - + +
87B ALA* 5.4 2.0 - - + -
88B VAL* 3.8 18.6 - - + -
120B GLY* 5.0 10.3 - - - +
121B LEU* 4.4 3.0 - - + +
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Residues in contact with VAL 48 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46B ASP* 2.7 12.0 + - - +
47B ILE* 1.3 77.2 - - + +
49B ALA* 1.3 59.2 + - - +
51B ALA* 3.3 4.7 + - - +
52B ARG* 2.9 30.6 + - + +
87B ALA* 4.5 23.8 - - + +
88B VAL* 5.9 0.9 - - - +
91B GLU* 5.1 20.2 - - + +
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Residues in contact with ALA 49 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44B PRO* 4.4 8.3 - - + -
46B ASP* 2.6 34.2 + - + +
48B VAL* 1.3 75.5 - - - +
50B GLN* 1.3 57.4 - - - +
52B ARG* 3.2 4.1 + - - +
53B GLN* 3.0 44.9 + - - +
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Residues in contact with GLN 50 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35B PRO* 3.1 31.9 - - + +
43B VAL* 3.0 25.7 - - - +
44B PRO* 2.5 38.2 - - + +
45B ALA* 3.2 17.2 - - - +
46B ASP 2.7 15.0 + - - +
47B ILE* 3.2 25.1 - - - +
49B ALA* 1.3 74.5 - - - +
51B ALA* 1.3 59.3 + - - +
53B GLN* 4.5 1.3 - - - -
54B SER* 3.1 23.0 + - - -
120B GLY* 3.7 16.8 - - - -
121B LEU* 3.4 17.6 - - + +
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Residues in contact with ALA 51 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47B ILE 2.8 23.6 + - - +
48B VAL* 3.6 6.7 - - - +
49B ALA 3.2 0.2 - - - -
50B GLN* 1.3 79.7 - - - +
52B ARG* 1.3 60.1 + - - +
54B SER* 4.0 3.4 - - - -
55B LEU* 3.5 28.4 + - + +
88B VAL* 4.1 29.1 - - + +
91B GLU* 5.4 3.6 - - - +
121B LEU* 3.7 15.9 - - + -
123B ILE* 4.7 1.4 - - - +
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Residues in contact with ARG 52 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48B VAL* 2.9 18.1 + - + +
49B ALA* 3.2 5.8 + - - +
51B ALA* 1.3 76.7 - - - +
53B GLN* 1.3 74.6 + - - +
55B LEU* 3.2 17.4 + - - +
56B GLU* 3.1 63.9 + - - +
59B LYS* 5.9 2.4 - - - +
91B GLU* 3.7 30.6 + - - +
95B PHE* 5.5 11.3 - - - +
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Residues in contact with GLN 53 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35B PRO* 4.7 11.2 - - + +
36B VAL 5.7 1.1 - - - +
37B ASN* 5.6 0.2 - - - -
38B PRO* 4.1 30.7 - - + +
44B PRO* 4.6 8.6 - - + +
49B ALA* 3.0 30.9 + - - +
50B GLN* 4.0 6.7 - - - +
52B ARG* 1.3 86.3 - - - +
54B SER* 1.3 60.6 + - - +
56B GLU* 3.1 9.3 + - + +
57B ASN* 2.5 38.4 + - - +
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Residues in contact with SER 54 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33B GLN 4.3 0.2 - - - -
34B ILE* 3.8 9.6 + - - -
35B PRO* 3.8 18.0 - - - +
50B GLN 3.1 19.3 + - - -
51B ALA 4.0 2.7 - - - -
53B GLN* 1.3 76.8 - - - +
55B LEU* 1.3 58.8 + - - +
57B ASN* 3.5 7.5 + - - +
58B VAL* 2.8 31.9 + - - +
121B LEU* 3.3 17.8 - - - +
123B ILE* 2.9 33.4 - - - +
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Residues in contact with LEU 55 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51B ALA* 3.5 16.5 + - + +
52B ARG* 3.2 21.7 + - - +
53B GLN 3.2 0.4 - - - -
54B SER* 1.3 77.2 - - - +
56B GLU* 1.3 60.4 + - - +
58B VAL* 3.6 5.6 + - + +
59B LYS* 3.1 29.5 + - - +
88B VAL* 6.2 2.5 - - + -
91B GLU* 4.5 12.8 - - - +
92B TYR* 3.8 26.7 - - + -
95B PHE* 3.3 50.9 - - + -
96B PHE* 4.7 0.9 - - + -
123B ILE* 4.0 16.8 - - + -
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Residues in contact with GLU 56 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10B LYS* 4.4 24.0 - - + -
52B ARG* 3.1 43.2 + - - +
53B GLN* 3.1 13.5 + - + +
55B LEU* 1.3 75.6 - - - +
57B ASN* 1.3 56.3 + - - +
59B LYS* 3.3 9.8 + - - +
60B ALA* 2.6 38.1 + - + +
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Residues in contact with ASN 57 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10B LYS* 3.5 25.2 + - - -
11B ALA* 3.6 9.0 - - - +
12B PRO* 3.7 15.6 - - + +
33B GLN* 4.1 13.2 - - + -
34B ILE 4.5 11.2 + - - +
36B VAL* 5.2 10.6 + - - +
53B GLN* 2.5 36.8 + - - +
54B SER* 3.8 6.3 - - - +
55B LEU 3.3 0.2 - - - -
56B GLU* 1.3 79.1 - - - +
58B VAL* 1.3 60.2 + - - +
60B ALA* 3.3 6.8 + - - +
61B ILE* 3.0 33.3 + - - +
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Residues in contact with VAL 58 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30B THR* 3.4 31.3 - - + +
33B GLN* 3.4 29.2 - - + +
54B SER 2.8 25.0 + - - +
55B LEU* 3.9 7.0 - - + +
57B ASN* 1.3 75.8 - - - +
59B LYS* 1.3 58.5 + - - +
61B ILE* 3.8 1.8 + - - +
62B ILE* 3.0 37.3 + - + +
72B ILE* 5.8 3.1 - - + -
123B ILE* 3.4 34.3 - - + +
125B ALA* 5.0 5.6 - - + +
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Residues in contact with LYS 59 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52B ARG* 5.9 2.5 - - - +
55B LEU 3.1 18.7 + - - +
56B GLU* 3.8 11.4 - - - +
58B VAL* 1.3 76.0 - - - +
60B ALA* 1.3 56.9 + - - +
61B ILE 3.2 0.4 - - - -
62B ILE* 3.6 6.9 - - + -
63B GLU* 2.6 67.6 + - + +
68B THR* 4.2 13.1 - - - +
69B ALA* 4.0 39.0 - - + +
95B PHE* 5.8 3.6 - - + -
99B ASN* 3.4 25.2 + - - +
101B HIS* 4.2 9.6 + - + -
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Residues in contact with ALA 60 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8B THR* 4.0 3.6 + - - -
10B LYS* 3.3 44.4 - - + -
11B ALA 4.6 0.7 - - - +
56B GLU* 2.6 23.7 + - + +
57B ASN* 3.3 6.5 + - - +
59B LYS* 1.3 74.9 - - - +
61B ILE* 1.3 56.9 + - - +
63B GLU* 3.8 8.7 - - - +
64B LYS* 2.9 30.7 + - - +
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Residues in contact with ILE 61 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6B ILE* 3.5 14.7 - - + +
8B THR* 3.9 16.8 - - + -
11B ALA* 3.1 31.0 - - + -
20B GLN 4.1 7.4 - - - +
21B ALA* 3.2 35.0 - - + -
30B THR* 5.1 1.1 - - + -
33B GLN* 3.2 39.7 - - + +
57B ASN 3.0 19.5 + - - +
58B VAL* 3.9 4.0 - - - +
60B ALA* 1.3 74.1 - - - +
62B ILE* 1.3 67.4 + - + +
64B LYS* 3.3 3.6 + - - +
65B ALA* 3.2 20.8 + - - +
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Residues in contact with ILE 62 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6B ILE* 6.0 2.9 - - + -
28B VAL* 4.4 9.2 - - + -
30B THR* 3.2 29.8 - - + -
58B VAL* 3.0 30.1 - - + +
59B LYS* 3.3 8.2 + - + +
61B ILE* 1.3 75.9 - - + +
63B GLU* 1.3 60.1 + - - +
65B ALA* 3.3 8.1 + - + +
66B GLY 3.2 6.2 + - - -
67B LEU* 3.0 49.2 + - + +
68B THR 4.2 6.7 - - - +
69B ALA* 5.4 2.2 - - - -
72B ILE* 4.6 23.3 - - + -
125B ALA* 5.5 1.3 - - + +
127B ALA* 4.3 17.5 - - + -
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Residues in contact with GLU 63 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59B LYS* 2.6 51.7 + - - +
60B ALA* 3.8 8.0 - - - +
62B ILE* 1.3 70.6 - - - +
64B LYS* 1.3 60.8 + - - +
65B ALA 3.0 4.7 - - - -
66B GLY* 3.1 14.0 + - - -
67B LEU 3.6 14.1 + - - +
68B THR* 4.3 9.5 - - - +
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Residues in contact with LYS 64 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6B ILE* 5.6 0.2 - - - -
7B HIS* 3.4 23.5 + - - +
8B THR* 3.8 25.6 - - - +
9B GLU* 4.7 4.5 - - - +
60B ALA 2.9 18.3 + - - +
61B ILE 3.3 5.8 + - - +
63B GLU* 1.3 75.4 - - - +
65B ALA* 1.3 59.0 + - - +
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Residues in contact with ALA 65 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6B ILE* 4.1 21.1 - - + -
23B ASP* 4.4 17.1 - - - +
28B VAL* 5.1 5.4 - - + -
61B ILE 3.2 12.2 + - - +
62B ILE* 3.5 12.3 - - + +
63B GLU 3.0 0.8 - - - -
64B LYS* 1.3 79.8 - - - +
66B GLY* 1.3 57.0 + - - +
67B LEU* 5.7 1.1 - - + -
129B ARG* 4.0 11.6 + - - +
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Residues in contact with GLY 66 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62B ILE 3.2 0.6 + - - -
63B GLU 3.1 10.6 + - - -
65B ALA* 1.3 81.3 - - - +
67B LEU* 1.3 69.9 + - - +
129B ARG* 3.7 16.2 + - - +
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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
------------------------------------------------------------
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