Contacts of the helix formed by residues 46 - 62 (chain D) in PDB entry 1SCF
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 SER 46 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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44D TRP 3.4 0.8 - - - -
45D ILE* 1.3 81.3 - - - +
47D GLU* 1.3 65.8 + - - +
49D VAL* 3.5 9.2 - - - +
50D VAL* 3.2 29.6 + - - +
90D VAL* 4.2 21.6 - - - +
126D PHE* 5.4 1.8 - - - -
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Residues in contact with GLU 47 (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 VAL* 3.6 21.8 - - + -
44D TRP* 3.5 8.0 + - - +
45D ILE 3.4 0.2 - - - -
46D SER* 1.3 81.1 + - - +
48D MSE 1.3 58.5 + - - +
50D VAL* 3.3 13.0 + - - +
51D GLN* 2.9 51.0 + - + +
104D SER* 4.2 8.3 + - - -
105D PRO* 3.3 21.5 - - + +
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Residues in contact with MSE 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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30D LEU* 3.5 28.5 - - + -
31D LYS 4.3 7.6 - - - +
32D TYR* 4.5 3.8 - - + -
33D VAL* 3.8 31.6 - - + +
36D MSE 3.9 9.6 - - - +
44D TRP* 3.0 35.0 + - + +
45D ILE 3.3 4.2 + - - +
47D GLU* 1.3 77.6 - - - +
49D VAL* 1.3 55.9 + - - +
51D GLN* 3.9 2.0 - - - +
52D LEU* 3.0 39.7 + - + +
118D ILE* 3.3 32.5 - - + -
122D SER* 3.5 18.8 - - - +
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Residues in contact with VAL 49 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45D ILE* 3.0 23.3 + - + +
46D SER* 3.5 15.9 - - - +
48D MSE 1.3 72.7 - - - +
50D VAL* 1.3 63.0 + - + +
52D LEU* 4.2 6.7 - - + -
53D SER 2.9 23.7 + - - -
83D VAL* 3.1 22.0 - - + +
86D LEU* 4.1 21.1 - - + +
87D VAL* 3.4 19.9 - - + +
90D VAL* 5.2 2.2 - - + -
122D SER* 5.1 0.4 - - - -
123D ILE* 4.6 7.9 - - + -
126D PHE* 3.5 37.9 - - + -
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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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46D SER 3.2 15.9 - - - +
47D GLU* 3.3 22.4 + - - +
49D VAL* 1.3 78.7 - - + +
51D GLN* 1.3 66.2 + - - +
53D SER* 3.5 3.6 + - - -
54D ASP* 3.3 20.8 + - - +
87D VAL* 4.0 28.3 - - + -
90D VAL* 6.2 1.8 - - + -
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Residues in contact with GLN 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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30D LEU* 3.5 8.5 - - + +
31D LYS* 3.2 61.6 + - + +
33D VAL* 5.3 0.2 - - + -
47D GLU* 2.9 47.2 + - + +
48D MSE 3.9 6.3 - - - +
50D VAL* 1.3 77.7 - - - +
52D LEU* 1.3 63.6 + - - +
54D ASP* 3.5 13.6 - - - +
55D SER* 3.1 28.6 + - - -
104D SER* 4.9 2.8 + - - -
105D PRO* 4.1 7.2 - - + +
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Residues in contact with LEU 52 (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 LEU* 3.9 26.7 - - + -
48D MSE 3.0 31.1 + - + +
49D VAL* 3.8 9.4 - - + +
51D GLN* 1.3 74.9 - - - +
53D SER* 1.3 64.5 + - - +
55D SER* 3.4 1.6 + - - +
56D LEU* 3.0 31.2 + - + +
83D VAL* 4.1 8.5 - - + -
115D PHE* 3.9 17.7 - - + +
119D PHE* 4.1 32.8 - - + +
122D SER* 3.5 31.6 - - - +
123D ILE* 4.5 9.4 - - + -
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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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49D VAL 2.9 20.7 + - - -
50D VAL* 3.8 5.2 - - - -
51D GLN 3.5 0.2 - - - -
52D LEU* 1.3 70.8 - - - +
54D ASP* 1.3 56.9 + - - +
56D LEU* 3.7 3.6 - - - +
57D THR* 2.8 39.9 + - - -
80D VAL* 5.1 3.7 + - - +
83D VAL* 3.7 17.5 - - - +
84D ASP* 3.4 22.5 + - - -
87D VAL* 4.2 11.8 - - - +
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Residues in contact with ASP 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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31D LYS* 5.9 3.8 - - - -
50D VAL 3.3 11.2 + - - +
51D GLN* 3.5 20.0 - - - +
52D LEU 3.2 0.4 - - - -
53D SER* 1.3 77.3 - - - +
55D SER* 1.3 61.0 + - - +
57D THR* 3.2 5.4 + - - -
58D ASP* 2.9 38.3 + - - +
1022D CA 2.6 28.5 - - - -
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Residues in contact with SER 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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28D ILE* 4.6 5.5 - - - +
29D THR 2.7 28.1 + - - -
30D LEU* 3.3 12.7 - - - +
31D LYS 4.6 0.3 + - - -
51D GLN* 3.1 16.7 + - - -
52D LEU 3.9 0.4 - - - -
54D ASP* 1.3 76.0 + - - +
56D LEU* 1.3 63.1 + - - +
58D ASP* 3.4 9.1 + - - +
59D LEU* 2.8 27.9 + - - +
115D PHE* 3.7 24.2 - - - -
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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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52D LEU 3.0 21.1 + - - +
53D SER 3.8 2.2 - - - +
55D SER* 1.3 79.3 - - - +
57D THR* 1.3 56.1 + - - +
59D LEU* 3.2 8.2 + - + +
60D LEU* 2.9 27.7 + - - +
76D ILE* 3.5 22.7 - - + +
79D LEU* 4.2 18.8 - - + +
80D VAL* 3.7 13.4 - - + +
83D VAL* 3.8 28.9 - - + -
115D PHE* 4.0 13.2 - - + -
116D PHE* 3.9 30.5 - - + -
119D PHE* 3.8 17.3 - - + -
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Residues in contact with THR 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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53D SER* 2.8 23.4 + - - -
54D ASP* 3.6 5.8 - - - -
56D LEU* 1.3 71.7 - - - +
58D ASP* 1.3 68.2 - - - +
60D LEU* 3.6 19.8 - - + +
61D ASP* 3.6 9.2 + - - +
80D VAL* 3.6 25.4 - - + +
84D ASP* 5.4 0.2 + - - -
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Residues in contact with ASP 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 ASP* 2.9 21.5 + - - +
55D SER* 3.7 7.5 - - - +
57D THR* 1.3 78.0 - - - +
59D LEU* 1.3 65.6 + - - +
61D ASP* 3.3 13.9 + - - +
62D LYS* 3.5 27.2 - - - +
1022D CA 2.8 26.3 - - - -
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Residues in contact with LEU 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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22D LEU* 4.9 5.4 - - + -
26D TYR* 3.4 40.2 - - + +
28D ILE* 4.1 31.0 - - + -
55D SER 2.8 21.5 + - - +
56D LEU* 3.2 12.8 + - + +
58D ASP* 1.3 71.3 - - - +
60D LEU* 1.3 63.5 + - - +
62D LYS* 2.9 23.2 + - - +
63D PHE* 3.4 15.9 - - + -
76D ILE* 3.9 24.5 - - + -
115D PHE* 5.4 0.9 - - + -
116D PHE* 4.1 18.6 - - + -
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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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56D LEU 2.9 16.2 + - - +
57D THR* 3.6 13.2 - - + +
59D LEU* 1.3 76.1 - - - +
61D ASP* 1.3 58.9 + - - +
62D LYS 3.1 1.4 + - - -
63D PHE* 3.3 21.6 + - - +
73D TYR* 3.4 66.8 - - + +
76D ILE* 3.9 10.5 - - + +
77D ASP* 3.5 30.7 - - + +
80D VAL* 4.5 14.4 - - + -
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Residues in contact with ASP 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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24C LYS* 3.2 24.9 + - - +
57D THR 3.6 8.0 + - - +
58D ASP* 3.3 13.2 + - - +
59D LEU 3.1 1.2 + - - -
60D LEU* 1.3 75.9 - - - +
62D LYS* 1.3 68.5 + - - +
63D PHE 3.3 1.1 - - - -
73D TYR* 5.8 0.2 - - - -
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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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22C LEU 3.6 2.9 - - - +
23C PRO* 3.4 17.2 - - + +
24C LYS* 2.9 46.5 + - + +
25C ASP* 2.9 37.6 + - + +
26D TYR* 3.7 16.1 + - - +
58D ASP* 3.5 23.4 + - - +
59D LEU* 2.9 17.1 + - - +
61D ASP* 1.3 90.5 - - - +
63D PHE* 1.3 59.1 + - + +
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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