Contacts of the helix formed by residues 23 - 35 (chain K) in PDB entry 4P5O
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 VAL 23 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22K LYS* 1.3 69.3 - - - +
24K GLU* 1.3 60.5 + - - +
25K ARG 3.0 7.0 + - - -
26K ILE* 3.2 25.7 + - + +
27K LYS* 3.6 5.0 + - - +
43K LEU* 4.0 9.0 - - + +
50K MET* 3.5 30.7 - - + -
51K ASN* 2.9 33.9 - - + +
52K ASP 3.1 14.6 - - - +
54K LYS 3.1 16.0 + - - +
55K THR 3.7 20.2 - - - +
56K ALA* 3.8 10.3 - - + +
59K TYR* 4.4 3.6 - - + -
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Residues in contact with GLU 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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22K LYS* 4.3 15.1 - - + +
23K VAL* 1.3 81.4 - - - +
25K ARG* 1.3 83.9 + - - +
27K LYS* 3.3 31.1 - - + +
28K GLU* 3.5 14.0 - - - +
38K PRO* 5.2 0.7 - - - +
52K ASP* 3.4 26.8 + - + +
53K GLU* 3.2 27.2 - - - +
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Residues in contact with ARG 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 ASP* 5.1 13.0 - - + +
22K LYS* 3.3 17.2 + - + +
23K VAL 3.0 0.4 - - - -
24K GLU* 1.3 105.7 + - + +
26K ILE* 1.3 61.6 + - + +
28K GLU* 2.6 67.3 + - - +
29K ARG* 3.0 33.2 + - + +
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Residues in contact with ILE 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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3K ILE* 4.2 17.0 - - + -
5K VAL* 5.1 0.2 - - + -
15K ILE* 3.6 26.0 - - + -
17K ILE* 4.0 25.8 - - + -
21K ASP* 5.9 3.8 - - + +
22K LYS 4.4 3.6 - - - +
23K VAL* 3.2 32.3 + - + +
25K ARG* 1.3 78.6 - - + +
27K LYS* 1.3 61.2 + - - +
29K ARG* 3.1 9.4 + - - +
30K VAL* 2.9 32.0 + - + +
43K LEU* 4.3 4.7 - - + -
50K MET* 4.8 3.8 - - + -
56K ALA* 4.8 11.4 - - + -
61K ILE* 5.2 2.2 - - + -
67K LEU* 4.4 17.3 - - + -
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Residues in contact with LYS 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 VAL 3.6 3.5 + - - +
24K GLU* 3.3 22.9 - - + +
26K ILE* 1.3 79.1 - - - +
28K GLU* 1.3 56.4 + - - +
30K VAL* 3.2 4.8 + - - +
31K GLU* 2.9 24.3 + - - +
38K PRO* 3.9 26.8 + - + +
39K GLN 5.7 0.4 + - - -
41K GLN* 3.0 54.3 + - + +
42K ARG* 4.9 6.1 - - - +
43K LEU* 3.7 29.6 - - + +
50K MET 5.5 2.4 + - - -
51K ASN 4.9 6.5 - - - -
52K ASP* 2.7 28.2 + - - -
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Residues in contact with GLU 28 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24K GLU* 3.5 13.5 - - - +
25K ARG* 2.6 52.7 + - - +
27K LYS* 1.3 72.1 - - - +
29K ARG* 1.3 62.4 + - - +
31K GLU* 3.1 5.0 + - - +
32K GLU* 2.9 27.9 + - - +
38K PRO* 4.1 24.4 - - + +
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Residues in contact with ARG 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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15K ILE* 4.4 22.7 - - + -
16K ASP* 2.8 50.6 + - - +
17K ILE* 5.2 0.9 - - + +
21K ASP* 5.2 7.2 + - - -
25K ARG* 3.0 36.1 + - - +
26K ILE* 3.1 12.3 + - + +
28K GLU* 1.3 75.7 - - - +
30K VAL* 1.3 57.9 + - - +
32K GLU* 3.3 21.2 + - - +
33K LYS* 3.0 33.0 + - - +
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Residues in contact with VAL 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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5K VAL* 4.8 16.4 - - + -
7K THR* 5.3 4.5 - - + -
15K ILE* 4.1 19.3 - - + -
26K ILE* 2.9 27.9 + - + +
27K LYS* 3.4 9.0 - - - +
29K ARG* 1.3 74.8 - - - +
31K GLU* 1.3 60.3 + - - +
33K LYS* 4.5 4.3 - - - +
34K GLU* 2.8 43.3 + - + +
36K ILE 4.5 0.2 + - - -
41K GLN* 3.2 19.5 - - - +
43K LEU* 4.9 8.1 - - + -
69K LEU* 4.1 16.4 - - + -
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Residues in contact with GLU 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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33B TRP* 5.7 1.2 - - - -
35B TRP* 3.6 27.4 + - + +
99B ARG* 4.9 8.3 + - - -
27K LYS 2.9 11.8 + - - +
28K GLU* 3.1 10.9 + - - +
30K VAL* 1.3 76.0 - - - +
32K GLU* 1.3 60.0 + - - +
35K GLY* 2.6 33.2 + - - -
36K ILE 3.1 36.7 + - - +
37K PRO* 4.1 5.2 - - - +
38K PRO* 3.2 28.1 - - + +
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Residues in contact with GLU 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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35B TRP* 3.6 52.3 - - + +
36B ASP 4.5 4.5 - - - +
28K GLU 2.9 12.7 + - - +
29K ARG* 3.4 24.7 - - - +
31K GLU* 1.3 78.5 - - - +
33K LYS* 1.3 68.4 + - + +
35K GLY 4.6 0.2 + - - -
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Residues in contact with LYS 33 (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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36B ASP 3.9 6.5 - - - +
37B ILE* 3.7 15.4 - - - +
38B VAL* 4.4 12.7 - - + +
13K ILE* 3.9 40.4 - - + -
14K GLU 4.8 7.0 - - - -
15K ILE* 4.5 8.5 - - + -
29K ARG 3.0 18.2 + - - +
30K VAL* 4.2 4.0 - - - +
32K GLU* 1.3 88.5 - - + +
34K GLU* 1.3 66.0 + - + +
35K GLY 3.6 0.2 - - - -
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Residues in contact with GLU 34 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B ILE* 3.4 11.2 - - - +
38B VAL* 3.6 25.0 - - - +
77B HIS* 3.0 22.0 + - - -
96B LEU* 5.9 0.7 - - - +
7K THR* 3.6 33.1 + - + -
9K THR* 3.6 26.6 + - - +
11K LYS* 6.0 1.2 - - - +
13K ILE* 3.0 28.5 - - + +
30K VAL* 2.8 28.4 + - + +
33K LYS* 1.3 71.6 - - + +
35K GLY* 1.3 61.4 + - - +
36K ILE* 3.3 13.5 + - + +
69K LEU* 6.0 1.3 - - + -
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Residues in contact with GLY 35 (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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35B TRP* 4.3 17.9 - - - -
37B ILE* 3.6 12.6 - - - +
75B CYS* 5.5 2.5 - - - +
77B HIS* 3.5 17.4 - - - -
97B ASP* 4.1 3.8 - - - +
99B ARG* 5.3 6.9 + - - -
31K GLU* 2.6 26.5 + - - -
32K GLU 4.6 0.2 - - - -
33K LYS 3.6 1.6 - - - -
34K GLU* 1.3 72.5 - - - +
36K ILE* 1.3 57.9 + - - +
37K PRO* 3.8 7.2 - - - +
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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