Contacts of the helix formed by residues 33 - 45 (chain K) in PDB entry 1XK4
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 ASN 33 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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26K LEU* 4.0 24.9 + - - +
27K GLY* 4.7 5.2 - - - +
31K THR* 3.8 2.0 + - - -
32K LEU* 1.3 75.5 - - - +
34K GLN* 1.3 64.5 + - - +
35K GLY* 3.3 5.5 + - - -
36K GLU* 2.9 46.1 + - - +
37K PHE* 3.0 21.3 + - - +
63K MET* 3.7 2.9 - - - -
72K LYS 4.0 11.2 - - - +
73K GLN* 4.5 7.2 - - + +
3522K CA 4.3 0.6 - - - -
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Residues in contact with GLN 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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33K ASN* 1.3 74.8 - - - +
35K GLY* 1.3 58.2 + - - +
37K PHE* 3.4 2.1 + - + +
38K LYS* 2.9 63.8 + - + +
60K GLU* 3.7 31.0 + - + +
63K MET* 3.7 25.7 - - + +
64K GLU* 5.2 5.5 + - - +
72K LYS 4.2 3.9 + - - +
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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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33K ASN* 3.3 6.8 + - - -
34K GLN* 1.3 77.7 - - - +
36K GLU* 1.3 58.6 + - - +
38K LYS* 3.4 9.8 + - - +
39K GLU* 3.0 30.8 + - - +
42K ARG* 5.5 0.3 + - - -
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Residues in contact with GLU 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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22K TYR* 3.2 30.3 - - + +
23K SER 3.5 0.5 - - - +
25K LYS* 3.8 8.3 - - + -
26K LEU* 2.7 42.9 + - + +
31K THR 3.4 3.6 - - - +
32K LEU* 3.6 13.9 - - + -
33K ASN* 2.9 32.9 + - - +
35K GLY* 1.3 73.4 - - - +
37K PHE* 1.3 66.1 + - - +
39K GLU* 3.4 7.3 + - - +
40K LEU* 3.0 24.9 + - - +
3522K CA 2.6 22.2 - - - -
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Residues in contact with PHE 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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32K LEU* 4.1 22.3 - - + +
33K ASN 3.0 17.2 + - - +
34K GLN* 3.8 4.0 - - + +
36K GLU* 1.3 75.9 - - - +
38K LYS* 1.3 64.1 + - + +
40K LEU* 3.3 3.3 + - + +
41K VAL* 2.9 51.7 + - + +
49K LEU* 6.0 0.4 - - + -
59K ILE* 3.7 24.5 - - + -
60K GLU* 6.0 0.2 - - - -
62K ILE* 3.9 21.3 - - + -
63K MET* 3.6 39.0 - - + -
66K LEU* 4.1 5.4 - - + -
74K LEU* 3.5 23.6 - - + -
79K PHE* 4.4 7.2 - + - -
82K LEU* 3.9 18.8 - - + -
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Residues in contact with LYS 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 GLN* 2.9 41.2 + - + +
35K GLY* 3.6 8.3 - - - +
37K PHE* 1.3 77.2 - - + +
39K GLU* 1.3 57.6 + - - +
41K VAL* 3.6 1.4 + - - +
42K ARG* 3.0 49.0 + - - +
53K ASN* 4.8 0.9 - - - +
56K GLU* 2.6 39.1 + - + +
59K ILE* 3.9 23.2 - - + +
60K GLU* 2.6 44.0 + - - +
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Residues in contact with GLU 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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22K TYR* 3.6 15.8 - - + -
25K LYS* 3.1 34.9 + - - +
35K GLY 3.0 17.2 + - - +
36K GLU* 3.7 7.7 - - - +
37K PHE 3.2 0.2 - - - -
38K LYS* 1.3 74.9 - - - +
40K LEU* 1.3 65.9 + - - +
42K ARG* 3.2 20.1 + - - +
43K LYS* 3.0 47.7 + - - +
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Residues in contact with LEU 40 (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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5I LEU* 4.1 22.2 - - + -
18K THR* 4.1 17.3 - - + +
19K PHE* 4.2 6.7 - - - -
22K TYR* 3.7 35.1 - - + -
32K LEU* 4.2 14.6 - - + -
36K GLU 3.0 17.2 + - - +
37K PHE* 3.7 4.9 - - + +
39K GLU* 1.3 76.7 - - - +
41K VAL* 1.3 64.6 + - + +
44K ASP* 2.8 30.1 + - + +
45K LEU* 3.5 8.2 + - + -
79K PHE* 3.9 33.4 - - + -
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Residues in contact with VAL 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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37K PHE* 2.9 51.5 + - + +
38K LYS 4.0 2.9 - - - +
40K LEU* 1.3 77.4 - - + +
42K ARG* 1.3 62.3 + - - +
45K LEU* 3.2 33.5 + - + -
49K LEU* 3.5 27.8 - - + -
53K ASN* 3.1 32.8 + - - +
59K ILE* 3.9 17.7 - - + -
82K LEU* 4.8 0.4 - - + -
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Residues in contact with ARG 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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35K GLY 5.5 0.2 + - - -
38K LYS* 3.0 39.4 + - - +
39K GLU* 3.2 33.0 + - - +
41K VAL* 1.3 78.2 - - - +
43K LYS* 1.3 67.5 + - + +
46K GLN* 3.3 21.0 + - - +
53K ASN* 3.4 19.0 + - + +
56K GLU* 5.1 7.7 + - - +
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Residues in contact with LYS 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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3I THR* 3.4 3.6 - - - +
22K TYR* 3.8 21.5 + - - +
25K LYS* 5.4 4.6 - - - +
39K GLU* 3.0 40.4 + - + +
42K ARG* 1.3 88.7 - - + +
44K ASP* 1.3 68.5 + - - +
45K LEU 3.3 0.7 - - - -
46K GLN* 2.9 33.5 + - - +
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Residues in contact with ASP 44 (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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3I THR* 2.6 32.9 + - - +
5I LEU* 3.5 27.4 + - + +
6I GLU* 3.5 0.2 - - - +
18K THR* 3.8 12.0 - - + +
22K TYR* 2.7 42.0 + - - -
40K LEU 2.8 15.9 + - - +
43K LYS* 1.3 76.0 - - - +
45K LEU* 1.3 70.0 + - - +
46K GLN 3.6 0.7 - - - -
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Residues in contact with LEU 45 (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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5I LEU* 3.7 16.6 - - + -
6I GLU* 3.2 23.6 - - + +
9I LEU* 4.7 6.5 - - + -
40K LEU* 3.5 19.9 + - + -
41K VAL* 3.2 21.6 + - + +
44K ASP* 1.3 86.5 - - - +
46K GLN* 1.3 57.3 + - - +
48K PHE* 4.3 7.4 - - + -
49K LEU* 2.9 49.6 + - + +
53K ASN* 3.6 1.6 + - - -
82K LEU* 4.3 6.7 - - + -
83K MET* 4.2 11.7 - - + -
86K LEU* 3.7 31.6 - - + -
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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