Contacts of the helix formed by residues 21 - 32 (chain G) 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 ALA 21 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20G GLY* 1.3 69.7 - - - -
22G LYS* 1.3 59.4 + - - +
23G ASN 4.4 1.8 - - - +
24G ALA* 3.6 20.9 - - + +
25G ALA* 2.9 30.8 + - - +
45G PRO* 4.5 0.7 - - - -
190G GLU* 4.6 10.3 - - + +
228G VAL* 3.6 3.4 - - - +
229G LEU* 2.8 29.6 + - + +
230G PRO 3.8 8.7 - - - +
231G ASP* 3.5 15.8 - - - +
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Residues in contact with LYS 22 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20G GLY 3.2 3.6 + - - -
21G ALA* 1.3 70.6 - - - +
23G ASN* 1.3 83.4 + - - +
25G ALA* 3.4 1.8 + - - +
26G LEU* 3.1 42.9 + - + +
45G PRO* 4.1 9.9 - - + -
47G LEU* 4.1 25.4 - - + -
49G ASP* 3.0 28.0 + - - -
231G ASP* 3.1 9.8 + - - +
370G LEU* 3.5 17.5 - - - -
371G ARG* 3.8 20.0 - - - +
397G ARG 3.8 5.8 - - - +
398G GLY* 3.7 20.6 - - - -
501G EPZ 2.7 24.2 + - - +
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Residues in contact with ASN 23 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21G ALA* 3.2 2.2 - - - +
22G LYS* 1.3 104.9 + - - +
24G ALA* 1.3 55.6 + - - +
26G LEU* 4.7 2.1 - - - +
27G PRO* 3.1 23.3 - - - +
190G GLU* 3.3 27.0 - - + +
233G ILE* 5.9 0.8 - - - +
305G ASP* 4.1 8.7 + - - -
371G ARG* 4.3 12.6 - - - +
501G EPZ 3.2 60.5 + - - +
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Residues in contact with ALA 24 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21G ALA* 3.1 10.3 + - + +
23G ASN* 1.3 75.0 - - - +
25G ALA* 1.3 69.0 + - - +
26G LEU 3.2 1.3 - - - -
27G PRO* 2.9 13.0 - - - +
28G ILE* 3.1 24.1 + - + +
190G GLU* 3.8 13.4 - - + +
193G ASP* 4.1 10.8 - - + +
228G VAL* 3.6 17.9 - - + -
229G LEU* 3.7 22.2 - - + -
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Residues in contact with ALA 25 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21G ALA 2.9 15.7 + - - +
22G LYS 3.7 5.2 - - - +
24G ALA* 1.3 79.0 - - - +
26G LEU* 1.3 56.5 + - - +
28G ILE* 3.4 1.4 + - - +
29G LEU* 2.9 40.1 + - + +
44G VAL* 4.1 31.2 - - + -
45G PRO* 4.3 7.9 - - + -
50G VAL* 4.5 9.0 - - + -
228G VAL* 4.2 13.6 - - + +
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Residues in contact with LEU 26 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22G LYS* 3.1 27.7 + - + +
23G ASN* 5.0 1.6 - - - +
25G ALA* 1.3 77.9 - - - +
27G PRO* 1.3 66.7 - - + +
29G LEU* 3.4 5.1 + - + +
30G PHE* 3.0 31.3 + - + -
49G ASP* 4.0 32.3 - - + +
50G VAL* 4.2 16.2 - - + +
53G SER* 3.5 19.7 - - - +
90G MET* 3.9 25.1 - - + -
92G ALA* 4.1 16.8 - - + -
95G TRP* 4.2 10.5 - - + -
501G EPZ 4.5 9.2 - - + -
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Residues in contact with PRO 27 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23G ASN 3.1 26.7 - - - +
24G ALA 2.9 20.4 - - - +
26G LEU* 1.3 81.1 - - + +
28G ILE* 1.3 60.5 + - - +
30G PHE* 3.2 4.9 + - + +
31G ALA* 2.8 28.9 + - - +
95G TRP* 3.5 32.1 - - + -
163G VAL* 6.5 0.2 - - + -
167G VAL* 4.1 22.1 - - + +
171G CYS* 5.3 1.6 - - - -
190G GLU* 5.3 2.5 - - + +
194G THR* 3.4 21.4 - - + +
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Residues in contact with ILE 28 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24G ALA* 3.1 21.2 + - + +
25G ALA* 3.7 3.8 - - - +
27G PRO* 1.3 77.1 - - - +
29G LEU* 1.3 62.9 + - - +
31G ALA* 3.0 17.9 + - - +
32G ALA* 3.0 11.6 + - - +
41G ILE* 3.6 31.9 - - + -
193G ASP* 4.1 26.7 - - - +
194G THR* 4.0 18.4 - - - +
197G PHE* 3.7 30.3 - - + -
226G TYR* 4.2 5.2 - - + -
228G VAL* 3.9 22.2 - - + -
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Residues in contact with LEU 29 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25G ALA* 2.9 34.5 + - + +
26G LEU* 3.9 5.6 - - - +
27G PRO 3.3 0.4 - - - -
28G ILE* 1.3 75.6 - - + +
30G PHE* 1.3 60.9 + - + +
32G ALA* 3.4 16.1 - - - +
41G ILE* 4.4 25.8 - - + -
44G VAL* 5.0 1.6 - - + -
50G VAL* 4.1 27.4 - - + +
53G SER* 3.9 25.8 - - - -
54G MET* 4.6 8.7 - - + -
57G LEU* 3.6 24.8 - - + +
70G VAL* 4.6 9.9 - - + -
72G ILE* 4.0 23.8 - - + -
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Residues in contact with PHE 30 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26G LEU* 3.0 27.0 + - + -
27G PRO 3.2 6.1 + - - +
28G ILE 3.1 0.8 - - - -
29G LEU* 1.3 74.6 - - - +
31G ALA* 1.3 64.5 + - - +
32G ALA 3.1 2.0 - - - -
33G LEU* 3.3 17.5 + - + +
53G SER* 3.7 30.5 - - - -
56G LEU* 3.5 35.2 - - + -
57G LEU* 4.3 17.7 - - + -
90G MET* 4.2 10.3 - - + -
92G ALA* 4.2 10.8 - - + -
93G SER* 4.1 14.6 - - - -
95G TRP* 3.8 35.2 - + + +
96G ALA* 4.0 17.7 - - + -
99G PRO* 3.4 16.8 - - - +
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Residues in contact with ALA 31 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27G PRO 2.8 16.4 + - - +
28G ILE* 3.0 6.7 + - - +
30G PHE* 1.3 70.5 - - - +
32G ALA* 1.3 59.6 + - - +
33G LEU 3.0 2.7 - - - -
34G LEU* 2.9 31.7 + - - +
35G ALA 4.1 0.7 + - - -
99G PRO* 4.4 9.0 - - - -
171G CYS* 4.1 15.7 - - - -
194G THR* 4.6 2.2 - - + -
197G PHE* 3.9 19.5 - - + -
198G LEU* 3.9 19.6 - - + +
201G LEU* 5.0 1.6 - - - +
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Residues in contact with ALA 32 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28G ILE 3.0 9.4 + - - +
29G LEU 3.4 14.8 - - - +
30G PHE 3.1 0.4 - - - -
31G ALA* 1.3 72.4 - - - +
33G LEU* 1.3 55.3 + - - +
34G LEU 2.8 11.4 + - - -
35G ALA* 2.9 24.2 + - - +
39G VAL* 4.2 13.0 - - + -
41G ILE* 5.4 0.4 - - + -
57G LEU* 5.5 0.4 - - + -
72G ILE* 3.7 33.7 - - + -
74G ALA* 3.6 10.2 - - - +
197G PHE* 4.1 10.5 - - + -
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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