Contacts of the helix formed by residues 22 - 31 (chain K) in PDB entry 5LXY
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 THR 22 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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18I GLU* 5.3 8.7 - - - +
20I LYS* 5.9 5.8 - - - -
20K LYS 3.4 16.6 + - - +
21K VAL* 1.3 75.9 - - - +
23K GLU* 1.3 65.3 + - - +
24K GLU* 3.8 9.4 + - - +
25K LEU* 3.1 32.4 + - - +
26K LEU* 3.1 13.9 + - - +
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Residues in contact with GLU 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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22K THR* 1.3 74.8 - - - +
24K GLU* 1.3 61.5 + - - +
26K LEU* 3.4 8.4 + - - +
27K PHE* 3.3 21.3 + - - +
39K VAL* 3.6 30.7 - - - +
40K LYS* 4.3 15.0 - - - +
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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 THR* 3.2 9.0 - - - +
23K GLU* 1.3 78.1 - - - +
25K LEU* 1.3 61.2 + - - +
27K PHE* 3.7 7.3 + - - +
28K GLU* 3.6 18.2 + - - +
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Residues in contact with LEU 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 VAL* 4.8 7.4 - - + -
22K THR* 3.1 22.3 + - - +
24K GLU* 1.3 77.7 - - - +
26K LEU* 1.3 64.1 + - - +
27K PHE 3.3 0.2 + - - -
28K GLU* 3.4 6.6 + - + -
29K LEU* 3.2 23.0 + - + +
75K LEU* 4.8 15.0 - - + -
76K TYR* 3.6 32.8 - - + +
292L SER* 5.0 2.9 - - - +
294L GLU* 4.6 6.3 - - + +
295L LEU* 3.6 37.2 - - + +
298L ALA* 3.7 16.6 - - + -
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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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14K VAL* 6.5 0.4 - - + -
22K THR 3.1 11.4 + - - +
23K GLU* 3.4 10.5 + - - +
25K LEU* 1.3 76.1 - - - +
27K PHE* 1.3 63.0 + - - +
29K LEU* 4.6 3.6 - - - -
30K PHE* 3.1 43.5 + - + +
39K VAL* 4.4 13.2 - - + -
53K ALA* 5.9 6.7 - - + -
75K LEU* 6.2 3.4 - - - -
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Residues in contact with PHE 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 GLU 3.3 10.8 + - - +
24K GLU* 3.8 11.9 - - - +
25K LEU 3.2 0.6 - - - -
26K LEU* 1.3 79.0 - - - +
28K GLU* 1.3 62.2 + - + +
29K LEU 3.2 0.2 + - - -
30K PHE* 3.7 0.3 - - - +
31K HIS* 2.8 72.6 + + - +
36K VAL* 3.5 42.0 - - + +
37K ILE 4.1 8.7 - - - -
38K LYS* 4.8 9.6 - - - -
39K VAL* 4.3 7.8 - - + +
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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
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24K GLU 3.6 9.0 + - - +
25K LEU* 3.4 14.8 + - + +
27K PHE* 1.3 83.9 - - + +
29K LEU* 1.3 63.6 + - - +
31K HIS* 3.6 14.9 - - - +
32K GLN* 3.9 11.4 + - - +
291L ILE* 5.4 5.8 - - + +
292L SER* 5.3 12.8 - - - +
295L LEU* 5.5 4.0 - - + -
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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 LEU* 3.2 17.6 + - + +
26K LEU* 3.9 5.6 - - - +
27K PHE 3.2 0.6 - - - -
28K GLU* 1.3 77.7 - - - +
30K PHE* 1.3 77.0 + - + +
32K GLN* 3.1 37.9 + - - +
70K LEU* 3.8 29.0 - - + +
73K ILE* 4.5 13.2 - - + -
75K LEU* 4.1 33.0 - - + -
80K ILE* 4.7 6.3 - - + -
291L ILE* 6.0 1.3 - - + -
295L LEU* 6.1 4.2 - - + +
299L LEU* 5.1 16.6 - - + -
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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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12K LEU* 5.5 5.8 - - + -
13K PHE 6.5 0.2 - - - -
14K VAL* 4.1 22.4 - - + -
26K LEU* 3.1 36.8 + - + +
29K LEU* 1.3 84.3 - - + +
31K HIS* 1.3 62.1 + - - +
32K GLN 3.0 6.1 - - - -
33K ALA* 3.0 14.3 + - - +
34K GLY 3.3 10.0 + - - +
36K VAL* 3.6 9.6 - - + -
55K VAL* 4.6 18.4 - - + -
57K PHE* 3.6 33.1 - + + -
66K ALA* 4.3 6.7 - - + -
70K LEU* 3.6 20.6 - - + -
80K ILE* 4.1 15.3 - - + -
82K ILE* 3.9 32.8 - - + -
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Residues in contact with HIS 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 PHE* 2.8 56.0 + + - +
28K GLU* 3.6 11.0 - - - +
29K LEU 3.1 0.6 - - - -
30K PHE* 1.3 76.2 - - - +
32K GLN* 1.3 55.6 + - - +
34K GLY 3.3 5.4 + - - +
35K PRO* 4.2 2.0 - - + -
36K VAL* 3.5 26.9 + - - +
286L PHE* 3.9 3.7 - + - -
322L TRP* 3.0 64.9 + + - -
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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