Contacts of the helix formed by residues 21 - 32 (chain K) 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 K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19K SER 3.6 0.8 + - - -
20K GLY* 1.3 69.1 - - - -
22K LYS* 1.3 65.4 + - - +
23K ASN 4.5 1.1 - - - +
24K ALA* 3.4 7.6 - - + +
25K ALA* 2.8 24.7 + - - +
190K GLU* 4.7 10.5 - - - +
228K VAL* 3.5 4.3 - - - +
229K LEU* 2.7 37.6 + - + +
230K PRO 3.4 13.2 - - - +
231K ASP* 3.5 14.8 - - + +
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Residues in contact with LYS 22 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20K GLY 3.2 5.1 + - - -
21K ALA* 1.3 67.9 - - - +
23K ASN* 1.3 68.5 + - - +
24K ALA 2.8 7.3 + - - -
25K ALA* 2.8 19.0 + - - +
26K LEU* 3.0 35.6 + - + +
45K PRO* 4.3 4.3 - - + -
47K LEU* 4.4 17.0 - - + -
49K ASP* 3.0 23.6 + - + +
231K ASP* 3.1 9.7 + - - +
370K LEU* 3.7 7.7 - - - +
371K ARG* 3.7 20.9 - - - +
397K ARG 3.1 24.2 - - - +
398K GLY* 3.6 17.3 - - - +
501K EPZ 2.9 30.4 + - - +
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Residues in contact with ASN 23 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21K ALA* 3.3 1.6 - - - +
22K LYS* 1.3 97.0 + - - +
24K ALA* 1.3 56.3 + - - +
26K LEU* 5.0 1.1 - - - +
27K PRO* 3.1 23.0 - - - +
95K TRP* 4.8 0.5 - - - -
190K GLU* 3.5 29.7 - - + +
233K ILE* 5.5 1.4 - - - +
305K ASP* 3.8 12.1 + - - -
371K ARG* 4.1 14.8 - - - +
501K EPZ 3.0 60.0 + - - +
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Residues in contact with ALA 24 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21K ALA* 2.9 12.3 + - + +
22K LYS 2.8 1.2 + - - -
23K ASN* 1.3 73.0 - - - +
25K ALA* 1.3 67.6 + - - +
27K PRO* 3.0 14.9 - - - +
28K ILE* 3.2 24.1 + - + +
190K GLU* 3.9 11.8 - - + +
193K ASP* 3.8 13.0 - - + +
194K THR* 4.5 0.2 + - - -
228K VAL* 3.6 9.4 - - + -
229K LEU* 3.5 31.4 - - + -
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Residues in contact with ALA 25 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21K ALA 2.8 11.8 + - - +
22K LYS* 2.8 10.5 + - - +
24K ALA* 1.3 77.4 - - - +
26K LEU* 1.3 67.6 + - + +
28K ILE* 3.2 2.4 + - - -
29K LEU* 3.0 34.7 + - + +
44K VAL* 4.0 27.8 - - + -
45K PRO* 4.1 8.7 - - + -
50K VAL* 4.7 3.1 - - + -
228K VAL* 4.3 13.2 - - + +
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Residues in contact with LEU 26 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22K LYS* 3.0 47.1 + - + +
25K ALA* 1.3 79.4 - - + +
27K PRO* 1.3 62.1 - - + +
29K LEU* 3.4 4.0 + - + +
30K PHE* 2.8 38.0 + - + -
49K ASP* 3.8 22.4 - - + -
50K VAL* 4.6 7.2 - - + +
53K SER* 3.8 15.3 - - - +
90K MET* 3.5 30.5 - - + -
92K ALA* 3.8 17.3 - - + -
95K TRP* 4.2 9.2 - - + -
501K EPZ 4.5 6.7 - - + -
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Residues in contact with PRO 27 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23K ASN 3.1 24.9 - - - +
24K ALA 3.0 11.9 - - - +
26K LEU* 1.3 92.3 - - + +
28K ILE* 1.3 58.1 + - - +
30K PHE* 3.3 5.4 + - + +
31K ALA* 2.9 27.1 + - - +
95K TRP* 3.3 31.9 - - + -
167K VAL* 4.2 19.9 - - + +
190K GLU* 5.3 1.3 - - + +
194K THR* 3.3 24.8 - - + +
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Residues in contact with ILE 28 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24K ALA* 3.2 20.5 + - + +
25K ALA* 3.8 4.0 - - - +
27K PRO* 1.3 73.0 - - - +
29K LEU* 1.3 66.7 + - + +
31K ALA* 3.0 8.0 + - - +
32K ALA* 2.9 22.5 + - - +
41K ILE* 3.6 31.4 - - + -
193K ASP* 3.8 26.2 - - - +
194K THR* 4.2 18.4 - - - -
197K PHE* 3.7 26.8 - - + -
226K TYR* 3.9 21.5 - - + -
228K VAL* 4.2 11.4 - - + -
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Residues in contact with LEU 29 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25K ALA* 3.0 28.4 + - + +
26K LEU* 4.0 4.7 - - - +
28K ILE* 1.3 76.4 - - + +
30K PHE* 1.3 59.2 + - - +
32K ALA* 3.1 20.1 - - - +
33K LEU 3.9 2.1 + - - -
41K ILE* 4.2 31.6 - - + -
44K VAL* 4.8 4.9 - - + -
50K VAL* 3.9 30.5 - - + -
53K SER* 4.2 17.9 - - - -
54K MET* 4.2 15.9 - - + -
57K LEU* 3.9 21.5 - - + +
70K VAL* 4.3 9.4 - - + -
72K ILE* 3.9 17.5 - - + -
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Residues in contact with PHE 30 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26K LEU* 2.8 35.7 + - + -
27K PRO* 3.3 5.6 + - + +
28K ILE 3.1 0.4 - - - -
29K LEU* 1.3 75.0 - - - +
31K ALA* 1.3 63.3 + - - +
32K ALA 3.0 1.8 - - - -
33K LEU* 3.1 29.1 + - + +
53K SER* 3.6 33.9 - - - -
56K LEU* 4.5 16.4 - - + -
57K LEU* 4.6 9.6 - - + -
90K MET* 4.7 5.6 - - + -
92K ALA 4.4 9.4 - - - -
93K SER* 4.4 17.9 - - - -
95K TRP* 3.9 31.9 - + + +
96K ALA* 4.1 29.4 - - + -
99K PRO* 3.5 12.5 - - + +
171K CYS* 6.0 0.2 - - - -
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Residues in contact with ALA 31 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27K PRO 2.9 16.7 + - - +
28K ILE* 3.0 1.5 + - - +
30K PHE* 1.3 70.9 - - - +
32K ALA* 1.3 60.0 + - - +
33K LEU 3.0 7.3 + - - -
34K LEU* 3.1 26.3 + - - +
35K ALA 4.3 1.7 + - - -
99K PRO* 4.9 1.6 - - - -
171K CYS* 4.2 15.9 - - - -
194K THR* 5.0 2.2 - - + -
197K PHE* 3.5 26.0 - - + -
198K LEU* 3.8 19.3 - - + -
201K LEU* 4.4 5.9 - - - +
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Residues in contact with ALA 32 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28K ILE 2.9 10.4 + - - +
29K LEU* 3.1 17.0 - - - +
30K PHE 3.0 0.4 - - - -
31K ALA* 1.3 78.2 - - - +
33K LEU* 1.3 60.3 + - - +
34K LEU 3.1 1.6 + - - -
35K ALA* 3.3 16.3 + - - +
39K VAL* 4.4 11.8 - - + +
41K ILE* 5.0 0.9 - - + -
57K LEU* 5.2 0.4 - - + -
72K ILE* 3.4 36.5 - - + +
74K ALA* 3.6 13.1 - - - +
197K PHE* 4.3 9.4 - - + -
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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