Contacts of the helix formed by residues 48 - 63 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45B ASN* 3.2 27.3 + - + +
46B ILE 3.3 0.6 - - - -
47B SER* 1.3 80.0 - - - +
49B SER* 1.3 62.7 + - - +
50B PHE* 3.6 7.6 - - - +
51B GLU* 3.1 36.7 + - + +
52B MET* 3.1 25.1 + - - +
75B THR* 3.6 2.2 - - - -
81D SER* 2.7 23.4 + - - +
85D ALA* 5.4 2.3 - - - +
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Residues in contact with SER 49 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B SER 4.0 1.0 + - - -
48B ASP* 1.3 71.7 - - - +
50B PHE* 1.3 52.0 + - - +
52B MET* 3.4 3.5 + - - +
53B THR* 2.6 42.9 + - - -
74B ARG 3.0 24.3 + - - -
75B THR* 3.8 10.8 - - - +
78B MET* 4.1 16.6 - - - +
77D ASN* 4.0 7.1 + - - +
78D MET* 3.9 18.7 + - - -
81D SER* 3.1 19.9 + - - -
82D PHE* 4.3 0.7 - - - -
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Residues in contact with PHE 50 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48B ASP* 3.6 9.4 - - - +
49B SER* 1.3 78.3 - - - +
51B GLU* 1.3 67.0 + - + +
53B THR* 3.3 3.5 + - - -
54B TYR* 2.8 37.7 + + + +
57D CYS* 5.8 1.3 - - - -
81D SER* 3.1 17.9 + - - +
82D PHE* 3.5 47.0 - + + -
85D ALA* 3.9 19.3 - - + -
86D LEU* 3.9 28.9 - - + -
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Residues in contact with GLU 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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43B ILE 5.3 0.3 - - - +
44B VAL* 3.9 15.2 - - + +
45B ASN* 3.4 34.4 + - - +
48B ASP* 3.1 26.0 + - + +
49B SER 3.4 0.2 - - - -
50B PHE* 1.3 83.8 - - + +
52B MET* 1.3 66.8 + - - +
54B TYR* 3.2 7.6 + - - +
55B ARG* 3.0 27.5 + - - +
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Residues in contact with MET 52 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B LEU* 3.8 18.6 - - + +
44B VAL* 3.7 29.8 - - - -
45B ASN 3.7 7.6 - - - +
46B ILE* 3.8 10.5 - - + -
48B ASP 3.1 20.6 + - - +
49B SER* 3.7 2.9 - - - +
51B GLU* 1.3 75.0 - - - +
53B THR* 1.3 52.7 + - - +
55B ARG* 3.3 2.7 + - - +
56B PHE* 2.8 36.9 + - - +
70B PHE 3.5 20.0 - - - +
75B THR* 4.0 18.2 - - + +
78B MET* 3.0 23.5 - - + +
79B LEU* 3.1 35.9 - - + -
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Residues in contact with THR 53 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49B SER 2.6 26.2 + - - -
50B PHE 3.4 5.8 - - - -
52B MET* 1.3 77.7 - - - +
54B TYR* 1.3 62.8 + - - +
56B PHE* 4.0 2.4 - - - +
57B CYS* 3.0 29.6 + - - +
78B MET* 3.5 22.1 - - - +
82B PHE* 3.6 30.1 - - + -
306B LEU* 5.7 1.3 - - + -
53D THR* 4.0 17.7 + - + -
78D MET* 5.5 0.3 - - - +
82D PHE* 3.9 15.0 - - + -
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Residues in contact with TYR 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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50B PHE* 2.8 26.7 + + + +
51B GLU* 3.2 10.7 + - - +
53B THR* 1.3 78.7 - - - +
55B ARG* 1.3 97.7 + - + +
57B CYS* 3.8 3.4 - - - +
58B SER* 2.8 45.4 + - - -
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Residues in contact with ARG 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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12B LEU* 3.5 20.2 - - + -
42B ASP* 3.2 46.7 + - - +
43B ILE 4.4 10.9 + - - -
44B VAL* 4.0 20.4 - - + -
51B GLU* 3.0 18.4 + - + +
52B MET 3.8 2.0 - - - +
54B TYR* 1.3 104.6 + - + +
56B PHE* 1.3 60.6 + - - +
58B SER* 4.3 8.9 + - - -
59B GLN* 2.8 37.3 + - - +
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Residues in contact with PHE 56 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B LEU* 4.6 7.5 - - + +
52B MET 2.8 22.0 + - - +
53B THR* 4.0 4.7 - - - +
55B ARG* 1.3 71.0 - - - +
57B CYS* 1.3 61.4 + - - +
59B GLN* 3.8 2.0 - - - +
60B PHE* 2.9 31.5 + - + +
67B ILE* 4.0 25.8 - - + +
78B MET* 4.9 3.4 - - - -
79B LEU* 3.7 21.8 - - + -
82B PHE* 3.9 38.4 - + + -
83B CYS* 3.8 23.8 - - - -
86B LEU* 3.6 26.5 - - + -
88B VAL* 4.1 23.3 - - + -
90B PHE* 5.5 0.7 - - + -
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Residues in contact with CYS 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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53B THR* 3.0 23.7 + - - +
54B TYR* 3.8 4.0 - - - +
56B PHE* 1.3 79.4 - - - +
58B SER* 1.3 55.9 + - - +
60B PHE* 3.3 3.4 + - - +
61B SER* 3.0 30.2 + - - -
82B PHE* 3.7 16.2 - - - -
305B CYS* 1.8 58.0 - - + +
306B LEU* 4.2 9.4 - - - -
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Residues in contact with SER 58 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B ASP* 5.5 0.7 + - - -
54B TYR* 2.8 45.3 + - - -
55B ARG* 3.8 14.1 + - - -
57B CYS* 1.3 72.6 - - - +
59B GLN* 1.3 61.4 + - - +
61B SER* 2.9 20.9 + - - -
62B LYS* 3.1 15.4 + - - +
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Residues in contact with GLN 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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10B GLY* 3.2 21.2 - - - -
11B GLY 3.0 32.2 + - - +
12B LEU* 3.6 10.7 - - - +
40B GLN* 4.0 5.4 + - + +
42B ASP* 2.8 33.1 + - - +
55B ARG* 2.8 18.7 + - - +
56B PHE 3.9 3.1 - - - +
58B SER* 1.3 74.3 - - - +
60B PHE* 1.3 65.5 + - - +
62B LYS* 3.4 10.6 + - + +
63B GLY 3.3 5.4 + - - -
64B VAL* 3.2 42.6 + - + +
67B ILE* 3.9 16.1 - - + +
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Residues in contact with PHE 60 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56B PHE* 2.9 26.6 + - + +
57B CYS* 3.3 6.5 + - - +
59B GLN* 1.3 77.4 - - - +
61B SER* 1.3 61.0 + - - +
63B GLY* 3.4 2.8 + - - -
64B VAL* 4.3 5.3 - - - +
67B ILE* 5.8 0.9 - - + -
86B LEU* 4.2 36.3 - - + -
88B VAL* 3.6 31.2 - - + -
299B ARG* 2.8 64.3 + - - +
303B GLY* 3.8 22.9 - - - -
304B ASP 4.3 4.3 - - - -
305B CYS* 4.3 13.5 - - + -
311B VAL 4.9 4.9 - - - -
313B TRP* 4.7 7.6 - - + -
36C LYS* 4.2 15.9 - - - -
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Residues in contact with SER 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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57B CYS 3.0 13.2 + - - -
58B SER* 2.9 23.2 + - - -
60B PHE* 1.3 73.8 - - - +
62B LYS* 1.3 58.7 + - - +
63B GLY 3.1 5.7 + - - -
300B GLY 4.0 2.6 - - - +
301B ASN 3.2 24.9 - - - +
302B ALA* 5.3 1.6 - - - -
303B GLY 2.9 33.2 + - - +
304B ASP* 5.2 2.7 - - - -
305B CYS 5.4 0.4 - - - -
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Residues in contact with LYS 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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8B GLN* 5.6 5.2 - - + +
40B GLN* 2.5 54.0 - - + +
58B SER* 3.1 12.9 + - - +
59B GLN* 3.4 19.5 + - + +
61B SER* 1.3 75.7 + - - +
63B GLY* 1.3 58.6 + - - +
64B VAL* 4.1 7.2 - - + +
299B ARG 5.3 1.7 - - - +
301B ASN* 5.0 2.8 - - - -
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Residues in contact with GLY 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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8B GLN* 4.5 5.5 - - - +
59B GLN 3.3 2.2 + - - -
60B PHE 3.4 8.9 + - - -
61B SER 3.1 4.5 - - - -
62B LYS* 1.3 80.6 - - - +
64B VAL* 1.3 71.2 + - - +
65B TYR* 3.6 12.1 + - - -
299B ARG* 3.6 35.6 + - - +
300B GLY 5.2 0.7 - - - -
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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
------------------------------------------------------------
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