Contacts of the helix formed by residues 18 - 32 (chain B) in PDB entry 1SFX
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 LYS 18 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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17B PHE* 1.3 76.8 - - - +
19B PRO* 1.3 74.8 - - + +
20B SER* 4.1 8.1 - - - +
21B ASP* 2.9 33.8 + - - +
22B VAL* 3.5 3.9 + - - +
49B PHE* 4.0 18.2 - - + -
53B ARG* 3.4 45.9 - - - +
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Residues in contact with PRO 19 (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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9A VAL* 6.4 0.2 - - + -
17B PHE 4.2 3.6 - - - +
18B LYS* 1.3 86.4 - - + +
20B SER* 1.3 61.3 + - - +
22B VAL* 3.2 21.2 + - + +
23B ARG* 3.2 19.6 + - - +
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Residues in contact with SER 20 (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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18B LYS* 3.1 3.9 - - - +
19B PRO* 1.3 81.0 - - - +
21B ASP* 1.3 56.9 + - - +
23B ARG* 3.2 12.1 + - - +
24B ILE* 2.8 37.6 + - - +
43B LEU* 4.9 0.2 - - - +
45B LEU* 3.6 24.6 - - - +
49B PHE* 3.4 36.5 - - - -
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Residues in contact with ASP 21 (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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5A LEU* 3.8 3.7 - - + +
16B SER 4.7 0.3 - - - +
17B PHE* 3.5 18.5 - - + +
18B LYS* 2.9 28.1 + - - +
20B SER* 1.3 77.3 - - - +
22B VAL* 1.3 59.5 + - - +
24B ILE* 3.3 4.6 + - - +
25B TYR* 3.0 30.7 + - - +
53B ARG* 2.8 56.5 + - - +
57B LEU* 4.2 29.6 - - + +
60B ARG* 5.5 0.3 + - - -
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Residues in contact with VAL 22 (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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3A ASN* 2.9 44.4 + - + +
5A LEU* 4.0 11.9 - - + -
6A GLY* 3.9 26.2 - - - +
9A VAL* 4.0 22.7 - - + -
17B PHE* 4.5 2.5 - - + -
18B LYS 4.1 9.4 - - - +
19B PRO* 3.2 12.0 + - + +
21B ASP* 1.3 76.6 - - - +
23B ARG* 1.3 59.0 + - + +
25B TYR* 3.5 0.5 + - - +
26B SER* 3.0 14.7 + - - -
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Residues in contact with ARG 23 (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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19B PRO* 3.2 14.8 + - - +
20B SER* 3.2 13.9 + - - +
22B VAL* 1.3 77.7 - - + +
24B ILE* 1.3 58.3 + - - +
26B SER* 3.5 6.7 + - - -
27B LEU* 3.0 28.9 + - - +
42B GLU 4.7 2.2 + - - -
43B LEU* 3.0 71.4 + - + +
45B LEU* 4.6 9.5 - - - +
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Residues in contact with ILE 24 (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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20B SER* 2.8 29.8 + - - +
21B ASP* 3.3 6.5 + - - +
23B ARG* 1.3 72.8 - - - +
25B TYR* 1.3 67.4 + - - +
27B LEU* 3.3 3.5 + - - +
28B LEU* 3.1 31.1 + - + +
39B ILE* 4.1 14.1 - - + +
43B LEU* 3.6 22.7 - - + -
45B LEU* 4.7 1.3 - - + -
49B PHE* 5.5 0.2 - - + -
50B VAL* 4.3 22.4 - - + +
53B ARG* 4.0 27.8 - - + -
54B LEU* 3.6 30.3 - - + -
57B LEU* 4.5 7.4 - - + -
63B VAL* 5.4 0.2 - - + -
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Residues in contact with TYR 25 (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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3A ASN* 3.8 16.2 - - - -
4A PRO* 3.5 26.2 - - + -
5A LEU* 3.7 22.2 - - + -
21B ASP 3.0 17.2 + - - +
22B VAL 3.8 2.9 - - - +
24B ILE* 1.3 80.3 - - - +
26B SER* 1.3 59.2 + - - +
28B LEU* 3.3 6.7 + - - +
29B LEU* 2.9 42.5 + - + +
57B LEU* 5.4 2.5 - - + -
62B PHE* 3.5 21.8 - - + -
63B VAL* 4.7 6.1 - - + -
79B ALA* 3.7 14.5 - - + +
80B GLU 2.7 28.8 + - - -
82B PRO* 3.4 26.5 - - - +
85B VAL* 3.7 9.3 - - + +
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Residues in contact with SER 26 (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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1A MSE 5.2 3.8 + - - -
3A ASN* 3.5 14.6 - - - +
22B VAL* 3.0 18.9 + - - -
23B ARG* 3.7 8.3 - - - -
24B ILE 3.3 0.2 - - - -
25B TYR* 1.3 78.7 - - - +
27B LEU* 1.3 57.4 + - - +
29B LEU* 3.3 4.5 + - - +
30B GLU* 2.9 50.6 + - - +
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Residues in contact with LEU 27 (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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23B ARG 3.0 19.3 + - - +
24B ILE* 3.7 4.9 - - - +
26B SER* 1.3 76.2 - - - +
28B LEU* 1.3 59.5 + - - +
30B GLU* 3.9 3.3 - - + +
31B ARG* 2.9 78.2 + - - +
34B MSE 3.7 30.1 - - + -
39B ILE* 3.9 22.4 - - + -
42B GLU* 3.9 19.7 - - + -
43B LEU* 4.1 14.6 - - + -
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Residues in contact with LEU 28 (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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24B ILE* 3.1 21.0 + - + +
25B TYR* 3.9 2.9 - - - +
27B LEU* 1.3 76.2 - - + +
29B LEU* 1.3 59.5 + - - +
32B GLY* 2.8 43.2 + - - +
34B MSE 3.9 11.7 - - + -
39B ILE* 3.8 23.3 - - + -
54B LEU* 4.1 24.7 - - + -
63B VAL* 4.2 9.0 - - + -
77B TYR* 3.4 30.1 - - + +
78B SER 4.1 12.6 - - - -
79B ALA* 3.8 17.2 + - + +
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Residues in contact with LEU 29 (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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1A MSE 3.7 34.4 - - + +
2A SER 4.6 10.8 - - - +
25B TYR* 2.9 43.1 + - + +
26B SER* 3.8 5.4 - - - +
28B LEU* 1.3 80.1 - - - +
30B GLU* 1.3 62.4 + - + +
32B GLY* 4.3 2.1 + - - -
79B ALA* 3.8 22.4 - - + +
80B GLU 4.5 1.8 - - - +
81B LYS* 5.2 2.0 - - - -
82B PRO* 4.3 22.7 - - + -
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Residues in contact with GLU 30 (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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0A HIS 3.2 12.8 + - - -
1A MSE 3.1 54.7 + - + +
26B SER* 2.9 40.0 + - - +
27B LEU* 3.9 4.7 - - + +
29B LEU* 1.3 79.4 - - + +
31B ARG* 1.3 68.6 + - + +
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Residues in contact with ARG 31 (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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27B LEU* 2.9 42.0 + - - +
30B GLU* 1.3 88.1 - - + +
32B GLY* 1.3 61.4 + - - +
33B GLY 5.1 0.7 - - - +
34B MSE 4.4 15.9 - - + +
42B GLU* 3.3 31.5 + - - +
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Residues in contact with GLY 32 (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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28B LEU* 2.8 29.7 + - - +
29B LEU 4.3 1.9 + - - -
30B GLU 3.8 0.8 - - - -
31B ARG* 1.3 79.0 - - - +
33B GLY* 1.3 68.0 + - - -
34B MSE 3.4 12.8 + - - +
78B SER* 5.0 2.0 - - - -
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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
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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