Contacts of the helix formed by residues 48 - 63 (chain D) in PDB entry 3SAJ
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 48 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81B SER* 3.3 18.3 + - - +
85B ALA* 5.3 1.9 - - - +
45D ASN* 3.0 27.1 + - - +
46D ILE 3.4 0.6 - - - -
47D SER* 1.3 77.6 - - - +
49D SER* 1.3 60.6 + - - +
50D PHE* 3.1 13.4 + - - +
51D GLU* 3.1 36.4 + - + +
52D MET* 2.9 33.1 + - - +
75D THR* 3.8 2.5 - - - -
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Residues in contact with SER 49 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B ASN* 3.7 15.2 + - - +
78B MET* 4.2 10.8 + - - -
81B SER* 3.6 19.6 + - - -
82B PHE* 4.3 3.1 - - - -
47D SER 3.8 1.2 + - - -
48D ASP* 1.3 71.2 - - - +
50D PHE* 1.3 54.6 + - - +
52D MET* 3.6 3.6 - - - +
53D THR* 2.7 39.0 + - - -
74D ARG 3.2 22.2 + - - -
75D THR* 3.7 12.8 - - - +
78D MET* 3.8 16.8 + - - +
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Residues in contact with PHE 50 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81B SER* 2.9 15.4 + - - +
82B PHE* 3.6 45.1 - + + -
85B ALA* 3.8 16.6 - - + -
86B LEU* 4.1 15.0 - - + -
305B CYS 3.5 24.5 - - - -
306B LEU* 4.1 7.7 - - + +
307B ALA 3.5 24.7 - - - -
310B ALA* 3.2 33.9 - - + -
48D ASP* 3.1 11.6 - - - +
49D SER* 1.3 73.7 - - - +
51D GLU* 1.3 76.7 + - + +
52D MET 3.0 0.9 - - - -
53D THR* 2.9 5.0 + - - -
54D TYR* 2.9 20.6 + - + +
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Residues in contact with GLU 51 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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308B ASN* 4.6 17.3 - - - +
16C GLN* 5.5 1.2 + - - +
44D VAL* 3.8 16.7 - - + +
45D ASN* 3.4 34.1 + - - +
48D ASP* 3.1 23.3 + - + +
50D PHE* 1.3 86.2 - - + +
52D MET* 1.3 57.3 + - - +
54D TYR* 3.2 8.1 + - - +
55D ARG* 2.9 32.4 + - + +
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Residues in contact with MET 52 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12D LEU* 3.5 34.0 - - + +
44D VAL* 3.6 27.8 - - - -
45D ASN 3.7 3.8 - - - +
46D ILE* 3.7 17.7 - - - +
48D ASP 2.9 26.1 + - - +
49D SER* 3.6 1.8 - - - +
51D GLU* 1.3 73.4 - - - +
53D THR* 1.3 58.6 + - - +
55D ARG* 4.1 1.5 - - - +
56D PHE* 3.0 31.4 + - - +
70D PHE 4.1 17.9 - - - +
75D THR* 3.7 17.5 - - + -
78D MET* 2.9 26.6 - - + +
79D LEU* 4.0 17.5 - - + -
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Residues in contact with THR 53 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53B THR* 4.0 13.0 + - + -
82B PHE* 3.8 16.7 - - + -
306B LEU* 3.9 20.2 - - + -
49D SER 2.7 26.2 + - - -
50D PHE 3.4 4.0 - - - -
52D MET* 1.3 73.4 - - - +
54D TYR* 1.3 64.2 + - - +
56D PHE* 3.8 2.3 - - - +
57D CYS* 3.0 25.2 + - - +
78D MET* 3.5 22.6 - - - +
82D PHE* 3.6 28.8 - - + -
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Residues in contact with TYR 54 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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306B LEU* 3.9 23.9 - - + +
307B ALA* 3.6 42.8 - - - +
308B ASN* 3.5 25.4 - - + +
40C GLN* 3.1 45.3 + - + +
62C LYS* 3.9 8.7 + - - -
50D PHE* 2.9 13.1 + - + +
51D GLU* 3.4 11.7 - - - +
53D THR* 1.3 77.1 - - - +
55D ARG* 1.3 90.3 + - + +
57D CYS* 3.9 1.4 - - - +
58D SER* 2.9 40.0 + - - -
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Residues in contact with ARG 55 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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308B ASN* 3.5 13.1 - - - +
40C GLN 5.6 0.2 - - - -
41C ILE 2.9 21.0 + - - -
42C ASP* 2.9 30.2 + - - +
43C ILE 5.0 1.4 - - - +
55C ARG* 4.6 0.6 - - - +
62C LYS* 4.8 5.7 - - - +
12D LEU* 3.4 22.9 - - + -
42D ASP* 2.6 46.3 + - + +
43D ILE 4.5 9.7 + - - -
44D VAL* 4.0 22.9 - - + -
51D GLU 2.9 17.9 + - - +
52D MET 4.1 1.8 - - - +
54D TYR* 1.3 94.7 + - + +
56D PHE* 1.3 57.2 + - - +
58D SER* 3.2 10.8 + - - -
59D GLN* 2.7 41.0 + - - +
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Residues in contact with PHE 56 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12D LEU* 4.5 15.1 - - + +
52D MET 3.0 20.3 + - - +
53D THR* 3.8 5.4 - - - +
55D ARG* 1.3 76.5 - - - +
57D CYS* 1.3 60.9 + - - +
59D GLN* 3.2 2.3 + - - +
60D PHE* 2.8 32.6 + - + +
67D ILE* 3.7 31.5 - - + +
78D MET* 5.0 6.5 - - + -
79D LEU* 5.1 8.1 - - + -
82D PHE* 3.9 40.4 - + + -
83D CYS* 4.0 21.5 - - - -
86D LEU* 3.6 27.4 - - + -
88D VAL* 4.3 17.9 - - + -
90D PHE* 5.5 2.9 - + + -
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Residues in contact with CYS 57 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50B PHE* 5.8 1.6 - - - -
306B LEU* 4.0 22.7 - - + -
53D THR* 3.0 20.6 + - - +
54D TYR 3.9 2.7 - - - +
56D PHE* 1.3 74.2 - - - +
58D SER* 1.3 58.1 + - - +
60D PHE* 3.5 8.5 - - - +
61D SER* 2.7 41.1 + - - +
82D PHE* 3.8 27.6 - - - -
86D LEU* 5.7 3.1 - - - -
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Residues in contact with SER 58 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62C LYS* 3.9 22.1 + - - +
42D ASP* 4.9 1.7 + - - -
54D TYR* 2.9 33.2 + - - -
55D ARG* 3.5 15.1 + - - -
57D CYS* 1.3 77.3 - - - +
59D GLN* 1.3 59.1 + - - +
61D SER* 3.5 6.0 + - - -
62D LYS* 2.8 31.6 + - - +
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Residues in contact with GLN 59 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10D GLY* 3.3 21.1 - - - -
11D GLY 2.9 33.2 + - - +
12D LEU* 3.8 9.5 - - - +
40D GLN* 3.8 9.2 + - + +
42D ASP* 3.5 27.0 + - - +
55D ARG* 2.7 23.7 + - - +
56D PHE 3.8 3.4 - - - +
58D SER* 1.3 74.2 - - - +
60D PHE* 1.3 61.9 + - - +
62D LYS* 3.3 8.2 + - + +
63D GLY 3.1 17.3 + - - -
64D VAL* 3.4 29.1 + - + +
67D ILE* 3.6 19.2 - - + +
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Residues in contact with PHE 60 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56D PHE* 2.8 26.0 + + + +
57D CYS* 3.2 11.4 + - - +
59D GLN* 1.3 76.3 - - - +
61D SER* 1.3 69.7 + - - +
63D GLY* 3.0 15.8 + - - -
64D VAL* 4.3 9.3 + - - +
67D ILE* 5.8 1.6 - - + -
86D LEU* 4.1 46.9 - - + -
88D VAL* 3.9 26.0 - - + -
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Residues in contact with SER 61 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57D CYS* 2.7 23.4 + - - +
58D SER* 3.7 6.7 - - - -
60D PHE* 1.3 80.3 - - - +
62D LYS* 1.3 60.7 + - - -
63D GLY* 3.2 2.1 + - - -
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Residues in contact with LYS 62 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54C TYR* 2.9 31.1 + - - -
55C ARG* 6.0 0.4 - - - +
58C SER* 3.1 27.7 + - - +
62C LYS* 6.3 9.2 - - + -
8D GLN* 5.9 2.1 - - - +
40D GLN* 3.1 39.0 - - + +
58D SER* 2.8 23.1 + - - +
59D GLN* 3.3 10.5 + - + +
61D SER* 1.3 71.6 - - - +
63D GLY* 1.3 58.6 + - - +
64D VAL* 3.8 2.7 - - + -
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Residues in contact with GLY 63 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8D GLN* 4.6 5.9 - - - +
59D GLN 3.1 1.2 + - - -
60D PHE 3.0 14.0 + - - -
61D SER 3.1 2.4 - - - -
62D LYS* 1.3 80.1 - - - +
64D VAL* 1.3 68.4 + - - +
65D TYR* 3.7 18.0 + - - -
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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