Contacts of the helix formed by residues 31 - 43 (chain K) in PDB entry 5ANC
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 GLY 31 (chain K).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26K ALA* 5.3 0.2 - - - -
29K ASP 3.9 0.4 + - - -
30K HIS* 1.3 85.7 + - - +
32K LYS* 1.3 59.0 + - - +
33K THR 3.6 0.4 - - - -
34K THR* 3.0 24.6 + - - -
35K LEU* 3.3 22.5 - - - +
63K GLU* 5.1 2.6 + - - -
64K GLN* 3.7 18.8 + - - -
116K VAL* 3.9 8.8 - - - +
146K ASN* 5.3 1.8 - - - -
235K THR* 5.7 1.1 - - - -
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Residues in contact with LYS 32 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24K VAL* 3.7 15.3 + - + +
25K LEU* 3.7 28.7 - - - +
26K ALA* 4.0 6.8 - - + +
29K ASP* 3.2 51.9 + - + +
30K HIS 3.3 0.8 - - - -
31K GLY* 1.3 75.4 - - - +
33K THR* 1.3 66.9 + - - +
34K THR 3.2 1.3 - - - -
35K LEU* 3.4 5.0 + - + +
36K ALA* 3.1 25.4 + - + +
57K MET* 4.3 9.2 - - + -
63K GLU* 3.9 7.1 + - - +
64K GLN* 4.3 0.4 + - - -
71K LYS* 5.5 4.0 - - - +
90K LEU* 4.9 0.7 - - + -
91K ILE 3.8 13.7 + - - -
92K ASP* 3.2 39.5 - - - +
93K SER 4.5 2.6 + - - +
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Residues in contact with THR 33 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32K LYS* 1.3 78.9 - - - +
34K THR* 1.3 57.0 - - - +
36K ALA* 3.3 1.4 + - - +
37K ASP* 2.9 37.4 + - + +
57K MET* 3.9 10.5 - - - +
58K ASP 4.7 0.3 + - - -
59K SER* 3.5 27.1 + - - +
60K ARG 3.0 33.9 + - - +
61K GLU* 5.3 1.8 - - - +
63K GLU* 4.1 9.9 + - - -
64K GLN* 3.6 15.4 + - + +
237K ALA* 4.4 18.6 - - + +
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Residues in contact with THR 34 (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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31K GLY* 3.0 19.7 + - - -
33K THR* 1.3 80.7 - - - +
35K LEU* 1.3 71.5 + - - +
37K ASP* 3.9 1.7 - - - +
38K CYS* 3.4 21.1 + - - +
64K GLN* 3.0 34.5 + - - +
147K LYS 5.6 0.2 - - - +
235K THR* 3.5 43.2 + - - +
236K SER* 3.8 6.4 - - - +
237K ALA* 3.7 27.6 - - + +
241K TRP 4.4 0.3 - - - +
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Residues in contact with LEU 35 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24K VAL* 3.7 31.9 - - + -
25K LEU 4.3 3.6 - - - +
26K ALA* 6.0 0.2 - - + -
31K GLY 3.3 20.9 - - - +
32K LYS* 3.4 4.4 + - - +
33K THR 3.3 0.4 - - - -
34K THR* 1.3 83.3 + - - +
36K ALA* 1.3 61.9 + - - +
38K CYS* 3.2 16.5 - - - -
39K LEU* 3.2 25.0 - - + +
114K ILE* 3.6 32.1 - - + -
116K VAL* 3.7 20.9 - - + -
144K VAL* 4.1 7.0 - - + -
233K VAL* 5.6 0.4 - - + -
235K THR* 3.8 27.4 - - + -
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Residues in contact with ALA 36 (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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32K LYS 3.1 18.3 + - - +
33K THR 3.8 0.2 - - - +
35K LEU* 1.3 76.5 - - - +
37K ASP* 1.3 60.4 + - - +
39K LEU* 3.2 10.8 + - - +
40K ILE* 2.9 36.7 + - + +
57K MET* 3.4 28.5 - - + -
90K LEU* 3.8 26.2 - - + +
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Residues in contact with ASP 37 (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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33K THR* 2.9 21.2 + - + +
34K THR 3.9 4.7 - - - +
36K ALA* 1.3 78.2 - - - +
38K CYS* 1.3 64.0 + - - +
40K ILE* 3.4 3.6 + - - +
41K SER* 3.3 25.8 + - - -
49K ARG* 4.7 8.9 + - - -
53K LYS* 3.9 25.1 + - - +
59K SER* 5.2 5.6 + - - +
237K ALA* 4.0 14.6 - - + +
240K GLY* 3.5 30.3 + - - -
241K TRP 4.5 1.0 + - - +
349K LEU* 5.1 1.7 - - - +
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Residues in contact with CYS 38 (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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34K THR 3.4 7.8 + - - +
35K LEU* 3.2 24.7 - - - -
36K ALA 3.2 0.4 - - - -
37K ASP* 1.3 80.8 - - - +
39K LEU* 1.3 64.0 + - - +
41K SER 3.9 0.2 + - - -
42K SER* 3.5 18.9 + - - -
235K THR* 6.3 2.0 - - - -
241K TRP 3.5 22.6 + - - +
242K GLY* 3.8 7.9 - - - -
349K LEU* 3.6 28.5 - - + +
351K ILE* 3.9 27.3 - - + +
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Residues in contact with LEU 39 (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 VAL* 3.8 29.6 - - + -
35K LEU* 3.2 21.1 - - + +
36K ALA* 3.2 10.5 + - - +
38K CYS* 1.3 84.0 - - - +
40K ILE* 1.3 64.2 + - - +
41K SER 3.2 0.4 - - - -
42K SER* 3.2 6.7 + - - -
43K ASN* 3.0 24.7 + - - +
77K LEU* 4.0 20.6 - - + -
79K TYR* 3.2 26.3 + - + +
88K ILE* 4.4 19.1 - - + -
90K LEU* 4.5 1.6 - - + -
114K ILE* 6.0 2.2 - - + -
351K ILE* 5.0 11.0 - - + -
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Residues in contact with ILE 40 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36K ALA* 2.9 26.4 + - + +
37K ASP* 3.8 4.9 - - - +
39K LEU* 1.3 77.0 - - + +
41K SER* 1.3 62.2 + - - +
43K ASN* 3.2 23.7 + - - +
46K ILE* 3.9 9.4 - - + +
48K SER 3.8 5.5 - - - +
49K ARG* 3.8 12.1 - - - -
52K GLY* 3.8 13.5 - - - -
53K LYS* 3.7 56.3 - - + +
57K MET* 4.3 18.2 - - + -
59K SER* 5.7 0.9 - - - +
75K ILE* 4.5 15.7 - - + -
77K LEU* 5.1 7.0 - - + -
90K LEU* 5.5 1.1 - - + -
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Residues in contact with SER 41 (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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1K MET 3.9 6.6 + - - +
37K ASP* 3.3 11.8 + - - -
38K CYS 3.9 8.3 - - - -
39K LEU 3.2 0.4 - - - -
40K ILE* 1.3 79.8 - - - +
42K SER* 1.3 64.5 + - - +
43K ASN 3.7 0.7 - - - +
48K SER* 3.7 16.4 + - - -
49K ARG* 3.2 42.3 - - - +
346K SER* 5.8 1.8 - - - -
349K LEU* 4.2 26.5 - - - +
350K PRO* 4.9 7.2 - - - +
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Residues in contact with SER 42 (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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1K MET* 2.8 37.7 + - - +
4K ASN* 5.0 0.2 + - - -
38K CYS 3.5 11.0 + - - -
39K LEU* 3.2 13.3 + - - -
41K SER* 1.3 78.7 - - - +
43K ASN* 1.3 56.8 + - - +
44K GLY 3.5 0.7 + - - -
79K TYR* 3.5 13.5 - - - -
350K PRO* 4.4 13.4 - - - +
351K ILE* 4.3 8.4 + - - +
352K SER* 2.7 36.6 + - - -
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Residues in contact with ASN 43 (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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1K MET 3.4 5.2 - - - +
39K LEU 3.0 14.1 + - - +
40K ILE 3.2 10.2 + - - +
41K SER 3.7 0.5 - - - +
42K SER* 1.3 75.8 - - - +
44K GLY* 1.3 65.7 + - - +
45K ILE* 3.4 29.4 + - - +
46K ILE* 3.7 19.6 - - + +
48K SER 3.4 19.2 + - - -
55K ARG* 4.2 0.2 - - - +
76K SER 3.4 5.5 + - - -
77K LEU* 3.2 32.6 - - + +
78K HIS 3.1 22.5 - - - +
79K TYR* 4.4 12.6 - - + -
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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