Contacts of the helix formed by residues 48 - 62 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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45A ASN* 3.0 30.1 + - + +
46A ILE 3.5 0.2 - - - -
47A SER* 1.3 79.3 - - - +
49A SER* 1.3 57.4 + - - +
50A PHE* 3.2 11.8 + - - +
51A GLU* 2.9 36.5 + - + +
52A MET* 3.0 29.6 + - - +
75A THR* 3.5 3.1 - - - -
81C SER* 2.9 22.0 + - - +
85C ALA* 5.2 3.4 - - - +
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Residues in contact with SER 49 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47A SER 3.9 0.8 + - - -
48A ASP* 1.3 71.0 - - - +
50A PHE* 1.3 55.1 + - - +
53A THR* 2.4 40.9 + - - -
74A ARG* 3.4 23.0 + - - +
75A THR* 3.4 13.5 - - - +
78A MET* 3.8 19.1 - - - +
77C ASN* 3.8 8.0 + - - +
78C MET* 4.0 19.1 + - - -
81C SER* 3.2 18.1 + - - -
82C PHE* 4.4 1.1 - - - -
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Residues in contact with PHE 50 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48A ASP* 3.2 10.1 + - - +
49A SER* 1.3 79.3 - - - +
51A GLU* 1.3 67.1 + - + +
53A THR* 3.3 2.8 + - - -
54A TYR* 2.9 27.1 + - + +
81C SER* 2.9 14.5 + - - +
82C PHE* 3.6 39.9 - + + -
85C ALA* 3.8 18.4 - - + -
86C LEU* 4.0 13.2 - - + -
305C CYS 3.4 27.6 - - - -
306C LEU* 3.8 18.5 - - + +
307C ALA 3.5 20.4 - - - -
310C ALA* 3.1 34.5 - - + -
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Residues in contact with GLU 51 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43A ILE 5.2 0.3 - - - +
44A VAL* 3.8 15.4 - - + +
45A ASN* 3.1 39.5 + - - +
48A ASP* 2.9 26.4 + - + +
50A PHE* 1.3 84.0 - - + +
52A MET* 1.3 62.4 + - - +
54A TYR* 3.2 8.9 + - + +
55A ARG* 3.0 26.7 + - - +
308C ASN* 4.4 19.0 - - - +
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Residues in contact with MET 52 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12A LEU* 3.7 19.4 - - + +
44A VAL* 3.7 23.6 - - - -
45A ASN 3.6 8.1 - - - +
46A ILE* 3.6 24.5 - - - +
48A ASP 3.0 19.6 + - - +
51A GLU* 1.3 76.0 - - - +
53A THR* 1.3 55.5 + - - +
55A ARG* 3.3 3.4 + - - +
56A PHE* 2.8 31.7 + - - +
70A PHE 3.4 18.8 - - - +
71A TYR* 4.3 0.4 - - - -
75A THR* 3.9 9.6 - - + +
78A MET* 2.8 28.3 - - + -
79A LEU* 3.3 34.8 - - + -
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Residues in contact with THR 53 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49A SER 2.4 27.4 + - - -
50A PHE 3.4 5.2 - - - -
52A MET* 1.3 75.5 - - - +
54A TYR* 1.3 60.0 + - - +
56A PHE* 4.3 4.5 - - - -
57A CYS* 2.9 44.5 + - - -
78A MET* 3.5 21.0 - - - +
82A PHE* 3.7 27.8 - - + -
53C THR* 4.1 5.7 + - + -
78C MET* 5.6 0.2 - - - +
82C PHE* 3.9 25.6 - - + -
306C LEU* 4.3 6.5 - - + -
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Residues in contact with TYR 54 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50A PHE* 2.9 16.0 + - + +
51A GLU* 3.5 11.2 - - + +
53A THR* 1.3 76.7 - - - +
55A ARG* 1.3 91.3 + - + +
57A CYS* 3.9 1.4 - - - +
58A SER* 2.8 43.6 + - - -
306C LEU* 3.8 27.1 - - + -
307C ALA* 3.7 36.3 - - - +
308C ASN* 3.3 33.2 + - + +
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Residues in contact with ARG 55 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12A LEU* 3.4 23.6 - - + -
42A ASP* 3.3 45.3 + - + +
43A ILE 4.5 12.9 + - - +
44A VAL* 3.8 19.0 - - + +
51A GLU 3.0 18.4 + - - +
52A MET* 3.6 2.2 - - - +
54A TYR* 1.3 98.7 + - + +
56A PHE* 1.3 55.1 + - - +
58A SER* 3.4 10.3 + - - -
59A GLN* 2.6 42.3 + - - +
308C ASN* 3.5 25.5 - - - +
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Residues in contact with PHE 56 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12A LEU* 4.7 9.0 - - + -
52A MET 2.8 22.0 + - - +
53A THR* 3.8 6.3 - - - +
55A ARG* 1.3 73.5 - - - +
57A CYS* 1.3 61.5 + - - +
59A GLN* 3.3 7.1 + - - +
60A PHE* 2.9 28.3 + - + +
67A ILE* 3.6 29.8 - - + +
78A MET* 5.4 0.9 - - - -
79A LEU* 4.2 21.3 - - + -
82A PHE* 3.9 41.3 - + + -
83A CYS* 4.0 21.1 - - - -
86A LEU* 3.8 26.0 - - + -
88A VAL* 4.1 18.8 - - + -
89A CYS 6.0 0.2 - - - -
90A PHE* 5.4 2.5 - + + -
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Residues in contact with CYS 57 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53A THR* 2.9 31.0 + - - +
54A TYR 3.9 2.7 - - - +
56A PHE* 1.3 75.6 - - - +
58A SER* 1.3 62.7 + - - +
60A PHE* 3.7 1.8 - - - +
61A SER* 3.0 30.9 + - - -
82A PHE* 3.6 16.2 - - - -
305A CYS* 2.7 48.4 - - + +
306A LEU* 4.3 4.3 - - - -
306C LEU* 4.1 19.7 - - + -
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Residues in contact with SER 58 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42A ASP* 5.6 0.7 - - - -
54A TYR* 2.8 40.6 + - - -
55A ARG* 3.4 16.8 + - - -
57A CYS* 1.3 77.1 - - - +
59A GLN* 1.3 64.1 + - - +
61A SER* 4.2 4.0 - - - -
62A LYS* 3.4 28.4 + - - +
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Residues in contact with GLN 59 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A GLY* 3.5 18.5 - - - -
11A GLY 3.1 29.8 + - - +
12A LEU* 3.9 11.4 - - - +
40A GLN 4.0 2.7 + - - +
42A ASP* 2.9 32.0 + - - +
55A ARG* 2.6 23.1 + - - +
56A PHE 3.8 3.4 - - - +
58A SER* 1.3 73.9 - - - +
60A PHE* 1.3 60.3 + - - +
62A LYS* 3.4 22.6 - - - +
63A GLY 3.4 13.9 + - - -
64A VAL* 3.4 25.4 + - + +
67A ILE* 3.5 25.3 - - + +
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Residues in contact with PHE 60 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56A PHE* 2.9 21.8 + - + +
57A CYS* 3.7 4.9 - - - +
59A GLN* 1.3 72.7 - - - +
61A SER* 1.3 63.5 + - - +
62A LYS 3.0 4.9 - - - -
63A GLY 3.0 3.6 + - - -
64A VAL* 4.6 2.4 - - - +
67A ILE* 5.3 2.0 - - + +
86A LEU* 3.9 32.8 - - + -
88A VAL* 3.5 30.1 - - + -
298A ARG* 2.5 53.5 + - - +
299A ARG* 5.3 6.2 - - - +
303A GLY* 3.6 22.7 - - - -
304A ASP 4.2 4.3 - - - -
305A CYS* 4.0 22.2 - - + -
311A VAL 4.9 6.3 - - - -
313A TRP* 4.7 7.9 - - + -
36D LYS* 4.4 9.6 - - - -
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Residues in contact with SER 61 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57A CYS 3.0 18.7 + - - -
58A SER* 4.2 5.2 - - - -
60A PHE* 1.3 76.7 - - - +
62A LYS* 1.3 59.2 + - - +
63A GLY 3.7 0.2 + - - -
300A GLY 3.9 1.0 - - - +
301A ASN 2.4 31.0 - - - +
302A ALA* 3.5 15.4 - - - -
303A GLY* 2.7 29.7 + - - +
304A ASP* 4.0 3.6 + - - -
305A CYS* 3.8 9.7 + - - +
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Residues in contact with LYS 62 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40A GLN* 3.9 36.9 + - - +
42A ASP* 4.6 8.1 + - - -
58A SER* 3.4 21.2 + - - +
59A GLN* 3.4 27.5 - - - +
60A PHE 3.0 0.2 - - - -
61A SER* 1.3 82.3 - - - +
63A GLY* 1.3 58.0 + - - +
64A VAL* 3.8 4.7 + - + -
299A ARG 4.3 5.1 - - - +
300A GLY* 4.3 12.7 - - - +
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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
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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