Contacts of the helix formed by residues 41 - 48 (chain K) in PDB entry 4PJO
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 ILE 41 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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43D LEU* 3.8 23.3 - - + +
45D ASN* 3.6 21.8 - - + +
51D LYS* 3.0 35.4 - - + +
108D VAL* 4.1 14.6 - - + -
110D LEU* 3.8 37.7 - - + -
29F TYR* 4.2 4.9 - - - +
49F GLU* 3.2 13.4 + - - +
59F LEU* 4.0 16.2 - - + -
40K GLY* 1.3 69.5 - - - -
42K ALA* 1.3 68.3 + - - +
43K PRO* 3.3 3.1 - - - -
44K TYR* 3.1 17.9 + - - +
45K ILE* 4.0 3.8 + - - +
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Residues in contact with ALA 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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49F GLU* 3.0 19.6 + - - +
56F SER* 3.5 17.3 - - - +
57F GLY* 3.8 25.4 - - - +
59F LEU* 4.2 13.7 - - + -
41K ILE* 1.3 79.1 - - - +
43K PRO* 1.3 68.3 - - + +
44K TYR 3.0 1.6 + - - -
45K ILE* 3.4 25.4 + - + +
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Residues in contact with PRO 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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49F GLU* 4.5 0.7 - - - +
51F ILE* 6.3 0.9 - - + -
56F SER* 5.0 3.6 - - - +
40K GLY 3.8 13.0 - - - +
41K ILE* 3.3 5.4 - - - +
42K ALA* 1.3 94.8 - - + +
44K TYR* 1.3 72.1 + - + +
45K ILE* 3.4 0.8 - - - +
46K ARG* 3.6 20.6 - - - +
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Residues in contact with TYR 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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43D LEU* 4.1 20.4 - - + +
51D LYS* 3.5 44.4 + - + +
53D LEU* 5.0 1.0 - - - +
73D MET* 3.9 43.1 - - + -
74D TRP* 4.5 16.5 - - - -
75D THR* 4.9 7.3 + - - -
91D ASN* 5.3 7.2 + - - -
39K CYS* 5.6 5.1 - - - -
40K GLY 3.9 6.3 - - - -
41K ILE* 3.1 13.7 + - - +
42K ALA 3.0 2.2 + - - -
43K PRO* 1.3 89.9 - - + +
45K ILE* 1.3 59.4 + - - +
46K ARG 3.2 2.9 - - - -
47K GLU* 2.9 31.3 + - + +
48K PHE* 4.3 1.6 + - - -
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Residues in contact with ILE 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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43D LEU* 5.1 0.4 - - + -
110D LEU* 4.2 15.5 - - + -
113D PRO* 4.8 10.3 - - + -
115D ILE* 5.0 9.3 - - + +
57F GLY* 6.1 0.7 - - - -
58F HIS 3.4 29.4 - - - +
59F LEU* 4.7 4.7 - - + -
41K ILE 4.0 5.8 + - - +
42K ALA* 3.4 18.6 + - + +
43K PRO 3.4 1.2 - - - -
44K TYR* 1.3 71.9 - - - +
46K ARG* 1.3 62.5 + - + +
47K GLU 2.8 11.8 + - - -
48K PHE* 2.9 45.1 + - + +
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Residues in contact with ARG 46 (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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43K PRO 3.6 21.1 - - - +
44K TYR* 4.4 1.3 - - - -
45K ILE* 1.3 81.5 - - + +
47K GLU* 1.3 78.6 + - + +
48K PHE 3.3 6.4 + - - +
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Residues in contact with GLU 47 (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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41D GLN* 4.4 2.3 + - - +
53D LEU* 3.4 23.0 - - + +
71D LYS* 3.3 25.8 + - - +
73D MET* 3.4 34.7 - - + +
44K TYR* 2.9 21.0 + - + +
45K ILE 2.8 1.6 + - - -
46K ARG* 1.3 95.5 + - + +
48K PHE* 1.3 65.3 + - - +
49K GLU* 3.6 1.0 + - - -
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Residues in contact with PHE 48 (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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41D GLN* 3.5 23.3 - - + -
43D LEU* 3.4 32.1 - - + -
53D LEU* 3.7 18.4 - - + +
110D LEU* 3.5 27.1 - - + -
112D ASN* 3.3 45.5 - - + +
113D PRO* 3.7 18.8 - - + -
115D ILE* 4.5 8.3 - - + +
44K TYR 4.7 1.1 - - - -
45K ILE* 2.9 35.2 + - + +
46K ARG 3.9 6.4 - - - +
47K GLU* 1.3 82.8 - - - +
49K GLU* 1.3 65.1 + - - +
50K ASP 3.8 0.3 + - - -
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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