Contacts of the helix formed by residues 29 - 62 (chain C) in PDB entry 5KHU
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 LEU 29 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28C ASP* 3.8 29.8 - - - +
30C ARG* 3.8 28.7 - - - +
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Residues in contact with ARG 30 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29C LEU* 3.8 26.2 - - - +
31C GLU* 3.8 28.9 - - - +
33C LYS* 4.4 15.7 - - - +
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Residues in contact with GLU 31 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30C ARG* 3.8 29.4 - - - +
32C ILE* 3.8 26.5 - - - +
34C LYS* 4.6 13.7 - - - +
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Residues in contact with ILE 32 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31C GLU* 3.8 24.7 - - - +
33C LYS* 3.8 29.8 - - - +
35C GLN* 4.6 14.4 - - - +
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Residues in contact with LYS 33 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30C ARG* 4.4 16.6 - - - +
32C ILE* 3.8 25.4 - - - +
34C LYS* 3.8 28.7 - - - +
36C LEU* 4.5 15.0 - - - +
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Residues in contact with LYS 34 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31C GLU* 4.6 14.8 - - - +
33C LYS* 3.8 26.2 - - - +
35C GLN* 3.8 28.5 - - - +
37C LEU* 4.7 14.1 - - - +
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Residues in contact with GLN 35 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32C ILE* 4.6 13.9 - - - +
34C LYS* 3.8 29.2 - - - +
36C LEU* 3.8 25.6 - - - +
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Residues in contact with LEU 36 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33C LYS* 4.5 15.9 - - - +
35C GLN* 3.8 25.8 - - - +
37C LEU* 3.8 29.6 - - - +
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Residues in contact with LEU 37 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34C LYS* 4.7 15.9 - - - +
36C LEU* 3.8 29.2 - - - +
38C LEU* 3.8 25.4 - - - +
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Residues in contact with LEU 38 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37C LEU* 3.8 28.3 - - - +
39C ILE* 3.8 29.2 - - - +
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Residues in contact with ILE 39 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38C LEU* 3.8 25.8 - - - +
40C ALA* 3.8 28.7 - - - +
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Residues in contact with ALA 40 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39C ILE* 3.8 28.0 - - - +
41C GLY* 3.8 29.4 - - - +
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Residues in contact with GLY 41 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40C ALA* 3.8 25.8 - - - +
42C LEU* 3.8 29.4 - - - +
44C ARG* 4.3 15.9 - - - +
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Residues in contact with LEU 42 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41C GLY* 3.8 30.1 - - - +
43C THR* 3.8 25.8 - - - +
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Residues in contact with THR 43 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42C LEU* 3.8 24.9 - - - +
44C ARG* 3.8 29.4 - - - +
46C ARG* 4.0 19.7 - - - +
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Residues in contact with ARG 44 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41C GLY* 4.3 18.4 - - - +
43C THR* 3.8 25.1 - - - +
45C GLU* 3.7 29.4 - - - +
47C GLY* 4.7 13.0 - - - +
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Residues in contact with GLU 45 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44C ARG* 3.7 25.4 - - - +
46C ARG* 3.7 29.8 - - - +
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Residues in contact with ARG 46 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43C THR* 4.0 19.7 - - - +
45C GLU* 3.7 29.8 - - - +
47C GLY* 3.8 24.7 - - - +
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Residues in contact with GLY 47 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44C ARG* 4.7 14.1 - - - +
46C ARG* 3.8 29.4 - - - +
48C LEU* 3.8 26.9 - - - +
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Residues in contact with LEU 48 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47C GLY* 3.8 26.7 - - - +
49C LEU* 3.7 30.3 - - - +
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Residues in contact with LEU 49 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48C LEU* 3.7 30.7 - - - +
50C HIS* 3.7 29.4 - - - +
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Residues in contact with HIS 50 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49C LEU* 3.7 29.6 - - - +
51C SER* 3.8 25.1 - - - +
53C LYS* 4.4 15.7 - - - +
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Residues in contact with SER 51 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50C HIS* 3.8 28.0 - - - +
52C SER* 3.7 30.1 - - - +
54C TRP* 4.6 13.0 - - - +
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Residues in contact with SER 52 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51C SER* 3.7 29.4 - - - +
53C LYS* 3.8 24.5 - - - +
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Residues in contact with LYS 53 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50C HIS* 4.4 17.7 - - - +
52C SER* 3.8 29.2 - - - +
54C TRP* 3.8 26.0 - - - +
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Residues in contact with TRP 54 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51C SER* 4.6 15.9 - - - +
53C LYS* 3.8 25.6 - - - +
55C SER* 3.8 29.6 - - - +
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Residues in contact with SER 55 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54C TRP* 3.8 26.9 - - - +
56C ALA* 3.7 29.6 - - - +
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Residues in contact with ALA 56 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55C SER* 3.7 30.1 - - - +
57C GLU* 3.8 28.3 - - - +
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Residues in contact with GLU 57 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56C ALA* 3.8 25.1 - - - +
58C LEU* 3.8 29.8 - - - +
60C PHE* 4.5 15.9 - - - +
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Residues in contact with LEU 58 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57C GLU* 3.8 26.2 - - - +
59C ALA* 3.7 29.6 - - - +
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Residues in contact with ALA 59 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58C LEU* 3.7 29.6 - - - +
60C PHE* 3.7 26.9 - - - +
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Residues in contact with PHE 60 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57C GLU* 4.5 16.4 - - - +
59C ALA* 3.7 29.8 - - - +
61C SER* 3.8 24.7 - - - +
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Residues in contact with SER 61 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60C PHE* 3.8 28.0 - - - +
62C LEU* 3.7 30.1 - - - +
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Residues in contact with LEU 62 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61C SER* 3.7 30.3 - - - +
63C PRO* 3.8 28.7 - - - -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
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