Contacts of the helix formed by residues 47 - 61 (chain D) in PDB entry 3SWD
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 LEU 47 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22D LYS* 4.1 19.1 - - + -
45D PRO* 3.2 25.4 + - + +
46D LYS* 1.3 75.3 - - - +
48D LYS* 1.3 67.4 + - - +
49D ASP* 3.3 2.2 - - + +
50D VAL* 3.0 42.2 + - + +
51D ASP* 3.4 17.1 + - - +
66D ARG* 4.7 0.6 - - - +
231D ASP* 5.9 0.4 - - - +
396D ASP 3.4 14.4 - - - +
397D ARG 3.7 11.9 - - - +
398D GLY* 3.5 31.0 - - - +
399D TYR 3.8 7.2 - - - +
400D GLU 3.9 10.3 - - - +
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Residues in contact with LYS 48 (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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47D LEU* 1.3 69.7 - - - +
49D ASP* 1.3 63.9 + - - +
51D ASP* 3.1 35.4 + - - +
52D THR* 3.1 22.6 + - - +
393D TYR 5.4 0.7 - - - +
396D ASP* 3.1 25.5 + - + +
397D ARG* 3.9 20.4 - - + -
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Residues in contact with ASP 49 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22D LYS* 3.0 29.1 + - - -
26D LEU* 4.0 21.8 - - + +
47D LEU* 3.3 3.7 - - + -
48D LYS* 1.3 77.1 - - - +
50D VAL* 1.3 59.2 + - - +
52D THR* 3.5 2.0 + - - -
53D SER* 3.0 26.5 + - - -
90D MET* 3.7 23.4 - - - +
370D LEU* 3.4 7.1 - - - +
397D ARG* 2.9 51.1 + - - +
501D EPZ 4.4 1.7 - - - +
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Residues in contact with VAL 50 (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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22D LYS 5.7 0.2 - - - +
25D ALA* 4.5 7.4 - - + -
26D LEU* 4.1 13.7 - - + -
29D LEU* 4.1 13.7 - - + -
44D VAL* 3.8 17.7 - - + -
45D PRO* 3.6 20.6 - - + +
47D LEU* 3.0 21.9 + - + +
49D ASP* 1.3 72.5 - - - +
51D ASP* 1.3 68.0 + - - +
53D SER* 3.1 8.5 + - - -
54D MET* 2.9 35.1 + - + +
66D ARG* 3.7 21.5 - - - +
70D VAL* 4.6 1.6 - - + -
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Residues in contact with ASP 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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47D LEU 3.4 15.1 + - - +
48D LYS* 3.1 33.3 + - + +
50D VAL* 1.3 78.4 - - - +
52D THR* 1.3 56.5 + - - +
54D MET* 3.1 27.3 + - + +
55D LYS* 2.9 27.9 + - - +
66D ARG* 4.7 5.5 + - - -
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Residues in contact with THR 52 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48D LYS* 3.1 25.3 + - - +
49D ASP* 3.8 8.5 + - - -
51D ASP* 1.3 76.1 - - - +
53D SER* 1.3 61.6 + - - +
55D LYS* 3.4 8.8 + - + -
56D LEU* 3.0 19.2 + - - +
86D LEU* 3.7 23.3 - - + +
89D THR* 3.9 21.5 + - - +
90D MET* 4.0 26.9 - - + +
93D SER* 5.0 0.9 - - - +
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Residues in contact with SER 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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26D LEU* 3.5 15.4 - - - +
29D LEU* 3.9 22.4 - - - -
30D PHE* 3.7 22.1 - - - -
49D ASP 3.0 14.8 + - - -
50D VAL* 3.1 9.5 + - - -
52D THR* 1.3 76.8 - - - +
54D MET* 1.3 56.2 + - - +
56D LEU* 3.2 4.2 + - - +
57D LEU* 2.9 33.8 + - - +
90D MET* 3.5 14.4 - - - +
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Residues in contact with MET 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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29D LEU* 4.6 5.2 - - + -
50D VAL* 2.9 23.0 + - + +
51D ASP* 3.2 37.9 - - + +
53D SER* 1.3 73.0 - - - +
55D LYS* 1.3 66.5 + - - +
57D LEU* 3.3 9.1 + - + +
58D SER* 2.8 27.2 + - - -
64D VAL* 3.9 29.6 - - + +
65D GLU* 5.0 1.8 - - - -
66D ARG* 3.7 39.7 - - + -
70D VAL* 4.3 10.8 - - + -
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Residues in contact with LYS 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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51D ASP 2.9 15.4 + - - +
52D THR* 3.8 9.6 - - + +
53D SER 3.3 0.2 - - - -
54D MET* 1.3 77.9 - - - +
56D LEU* 1.3 62.3 + - - +
58D SER* 3.4 6.1 + - - -
59D GLN* 3.0 39.2 + - + +
86D LEU* 4.0 24.5 - - + +
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Residues in contact with LEU 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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30D PHE* 3.5 28.5 - - + -
52D THR 3.0 9.9 + - - +
53D SER* 3.7 7.2 - - - +
55D LYS* 1.3 73.3 - - - +
57D LEU* 1.3 66.3 + - - +
59D GLN* 3.0 17.5 + - + +
60D LEU* 3.0 32.1 + - + +
81D CYS 4.5 0.2 - - - +
82D ALA* 4.0 31.4 - - + -
83D PRO* 4.3 7.6 - - + -
86D LEU* 3.3 25.5 - - + +
90D MET* 5.9 0.4 - - + -
93D SER* 3.8 30.3 - - - +
96D ALA* 4.3 4.0 - - + -
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Residues in contact with LEU 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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29D LEU* 3.6 39.7 - - + +
30D PHE* 4.3 17.5 - - + -
32D ALA* 5.7 0.2 - - + -
33D LEU* 4.0 29.2 - - + -
53D SER* 2.9 20.3 + - - +
54D MET* 3.5 9.9 - - + +
56D LEU* 1.3 73.9 - - - +
58D SER* 1.3 64.9 + - - +
60D LEU* 3.1 18.6 + - + +
61D GLY 3.4 0.5 + - - -
62D ALA* 3.2 23.8 + - + +
64D VAL* 3.8 15.5 - - + -
72D ILE* 3.9 25.6 - - + -
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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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54D MET 2.8 17.3 + - - -
55D LYS* 3.7 7.2 - - - -
57D LEU* 1.3 76.9 - - - +
59D GLN* 1.3 61.6 + - - +
61D GLY* 2.9 15.1 + - - -
62D ALA 3.6 16.6 + - - +
64D VAL* 4.3 9.3 - - - +
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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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55D LYS* 3.0 31.3 + - + +
56D LEU* 3.0 11.5 + - + +
58D SER* 1.3 76.1 - - - +
60D LEU* 1.3 53.0 + - + +
61D GLY* 3.2 1.0 + - - -
79D VAL* 2.6 27.8 - - + +
81D CYS 5.2 1.5 - - - +
83D PRO* 3.7 25.3 - - - +
86D LEU* 3.2 29.2 - - - +
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Residues in contact with LEU 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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33D LEU* 3.7 37.2 - - + -
56D LEU* 3.0 35.4 + - + +
57D LEU* 3.1 9.8 + - + +
59D GLN* 1.3 77.5 - - - +
61D GLY* 1.3 58.1 + - - +
62D ALA 3.6 0.4 - - - +
77D VAL* 3.3 13.1 - - + +
78D ASN 3.0 22.0 + - - -
79D VAL* 3.0 35.7 + - + +
81D CYS 3.7 35.4 - - - +
82D ALA* 5.1 0.4 - - - -
96D ALA* 4.6 4.3 - - + -
100D LEU* 4.2 15.0 - - + -
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Residues in contact with GLY 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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58D SER 2.9 10.9 + - - -
59D GLN 3.1 2.3 - - - -
60D LEU* 1.3 80.4 - - - +
62D ALA* 1.3 64.3 + - - +
63D LYS* 4.0 6.4 + - - +
73D ASP 4.6 0.2 - - - +
76D ASP* 3.3 25.2 + - - +
77D VAL* 4.1 3.1 - - - -
78D ASN* 3.7 15.9 - - - -
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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