Contacts of the helix formed by residues 49 - 57 (chain C) in PDB entry 4KZX
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 49 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111A GLN* 3.5 21.1 - - + +
118A GLU* 3.7 15.3 - - - -
47C PRO* 3.4 1.3 - - - +
48C VAL* 1.3 78.3 - - - +
50C LYS* 1.3 55.6 + - - +
51C LEU* 3.2 12.1 + - - +
52C GLY* 2.6 36.7 + - - -
53C ARG* 3.0 15.8 + - - +
74C LYS* 4.9 3.4 - - + +
75C GLU* 2.7 41.4 + - + +
78C ILE* 4.0 4.7 - - + +
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Residues in contact with LYS 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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118A GLU* 1.9 77.6 + - - +
119A PRO 5.2 0.2 + - - -
49C THR* 1.3 73.0 - - - +
51C LEU* 1.3 70.5 + - + +
53C ARG* 3.0 19.6 + - - +
251C TYR* 1.9 55.7 + - + -
258C LEU* 2.8 60.0 - - + +
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Residues in contact with LEU 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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49C THR* 3.2 7.1 + - - +
50C LYS* 1.3 89.4 - - + +
52C GLY* 1.3 57.5 + - - +
54C LEU* 3.4 2.9 + - - +
55C VAL* 2.9 25.8 + - + +
60C ILE* 3.2 27.6 - - + -
66C ILE* 3.9 16.2 - - + -
71C LEU* 4.2 22.4 - - + -
72C PRO 4.5 12.3 - - - +
73C ILE* 4.2 7.4 - - + -
78C ILE* 2.9 42.8 - - + -
258C LEU* 4.3 4.7 - - - -
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Residues in contact with GLY 52 (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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45C TRP* 3.8 6.9 - - - -
47C PRO* 4.2 5.6 - - - -
49C THR* 2.6 25.2 + - - -
51C LEU* 1.3 71.5 - - - +
53C ARG* 1.3 64.3 + - - -
55C VAL* 3.1 5.5 + - - +
56C LYS* 3.0 23.9 + - - +
75C GLU* 3.9 10.3 - - - -
78C ILE* 4.0 16.2 - - - -
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Residues in contact with ARG 53 (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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118A GLU* 4.9 2.6 + - - -
47C PRO* 3.9 24.3 + - + +
48C VAL 3.4 25.4 + - - -
49C THR 3.0 6.6 + - - +
50C LYS* 3.0 25.0 + - - +
52C GLY* 1.3 76.7 - - - +
54C LEU* 1.3 62.7 + - - +
56C LYS* 3.1 12.7 - - + +
57C ASP* 3.0 34.8 + - - +
257C HIS 4.5 8.5 - - - +
258C LEU* 2.5 48.9 + - + +
259C VAL* 4.5 3.2 - - - +
260C LYS* 4.8 18.5 - - + +
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Residues in contact with LEU 54 (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 LYS 3.2 1.7 + - - +
51C LEU* 3.7 4.9 - - - +
53C ARG* 1.3 77.1 - - - +
55C VAL* 1.3 56.3 + - - +
57C ASP* 4.5 0.4 - - - -
58C MET 3.3 1.4 + - - -
59C LYS* 2.7 23.1 + - + +
60C ILE* 2.6 50.0 + - + -
71C LEU* 6.4 0.4 - - + -
250C PRO 3.2 28.0 - - - +
251C TYR* 4.1 1.1 - - - +
254C PHE* 2.9 28.9 - - + +
257C HIS* 4.0 9.6 - - + +
258C LEU* 1.7 73.0 - - + +
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Residues in contact with VAL 55 (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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45C TRP* 4.6 6.7 - - + -
51C LEU* 2.9 35.4 - - + +
52C GLY* 3.3 7.9 - - - +
54C LEU* 1.3 74.3 - - - +
56C LYS* 1.3 66.3 + - - +
58C MET* 3.0 19.9 + - - +
60C ILE* 3.7 2.8 - - + +
78C ILE* 3.9 9.2 - - + +
81C PHE* 3.3 26.0 - - + -
82C PHE* 1.9 73.1 - - + -
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Residues in contact with LYS 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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44C GLU* 5.6 2.8 + - - -
45C TRP* 4.2 28.4 + - + -
46C LEU* 5.2 2.0 - - - +
47C PRO* 3.9 30.9 - - + +
52C GLY 3.0 14.0 + - - +
53C ARG* 3.1 18.2 - - - +
55C VAL* 1.3 78.4 - - - +
57C ASP* 1.3 80.5 + - - +
58C MET* 2.9 22.4 - - - +
81C PHE* 5.2 4.5 - - - -
260C LYS* 6.3 1.6 - - - +
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Residues in contact with ASP 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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53C ARG* 3.0 20.1 + - - +
54C LEU 3.9 4.5 - - - +
56C LYS* 1.3 102.8 - - - +
58C MET* 1.3 69.5 + - - +
59C LYS* 3.0 13.8 + - + +
257C HIS* 3.0 42.4 + - + +
260C LYS* 5.3 6.6 + - - -
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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