Contacts of the strand formed by residues 43 - 49 (chain L) in PDB entry 2ZPK
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 43 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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105H GLN* 6.2 1.8 - - - +
37L GLN 3.3 4.2 - - - +
38L GLU* 3.3 0.5 - - - -
39L LYS* 2.9 52.5 + - + +
40L PRO 4.1 11.7 - - - +
41L ASP 3.0 4.7 + - - +
42L HIS* 1.3 72.8 - - - +
44L PHE* 1.3 65.8 + - - +
45L THR* 3.8 19.9 + - - +
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Residues in contact with PHE 44 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39H LYS* 4.2 4.9 - - + -
45H LEU* 3.8 27.1 - - + -
91H PHE* 3.6 29.4 - + + -
103H TRP* 3.5 50.4 + + + +
104H GLY 5.1 2.9 + - - +
105H GLN* 6.3 0.2 - - - +
36L VAL* 4.0 19.3 - - + -
37L GLN 3.2 7.6 - - - -
38L GLU* 3.5 42.6 - - + -
42L HIS* 3.6 16.1 + - + -
43L LEU* 1.3 79.7 - - - +
45L THR* 1.3 61.1 + - - +
87L PHE* 3.8 19.7 - + - -
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Residues in contact with THR 45 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103H TRP* 4.4 3.4 - - - +
36L VAL* 3.4 2.0 - - - -
37L GLN* 2.9 53.4 + - - +
39L LYS* 6.0 0.2 - - - +
43L LEU* 3.8 15.4 + - - +
44L PHE* 1.3 75.7 + - - +
46L GLY* 1.3 77.4 + - - +
47L LEU* 3.5 13.9 + - + +
58L VAL* 4.5 7.4 - - + -
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Residues in contact with GLY 46 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99H PHE 3.9 14.8 - - - -
101H VAL 3.5 22.6 + - - -
103H TRP* 3.9 5.2 - - - -
35L TRP 4.1 4.5 - - - -
36L VAL* 4.2 3.8 - - - -
45L THR* 1.3 76.7 - - - +
47L LEU* 1.3 60.2 + - - -
48L ILE 5.8 0.2 - - - -
49L VAL* 6.1 0.4 - - - -
55L VAL* 3.5 15.4 - - - +
58L VAL* 3.4 17.8 - - - +
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Residues in contact with LEU 47 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35L TRP* 2.9 13.8 + - + +
36L VAL 4.2 2.9 - - - -
37L GLN* 3.8 17.9 - - + +
45L THR* 3.9 24.9 - - + +
46L GLY* 1.3 75.4 - - - -
48L ILE* 1.3 76.7 + - + +
54L ARG* 3.6 1.4 - - - -
55L VAL* 2.9 25.1 + - - +
58L VAL* 3.9 27.9 - - + +
59L PRO* 5.8 0.9 - - + -
62L PHE* 4.1 25.1 - - + -
73L LEU* 4.1 7.6 - - + -
86L TYR* 3.5 38.6 - - + -
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Residues in contact with ILE 48 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33L ALA 4.2 4.9 - - - +
34L ASN* 3.2 4.0 - - - +
35L TRP* 2.9 38.8 + - + +
36L VAL* 5.6 0.3 - - - +
46L GLY* 5.8 0.2 - - - -
47L LEU* 1.3 88.5 + - + +
49L VAL* 1.3 72.9 + - - +
51L THR 3.2 34.5 - - - +
52L ASN 3.8 4.7 - - - +
53L ASN 3.3 5.8 - - - +
54L ARG* 3.9 21.1 - - + +
55L VAL* 4.5 0.4 - - - -
62L PHE* 4.4 6.3 - - + +
63L SER* 3.9 11.4 - - - +
64L GLY* 3.7 18.4 - - - +
73L LEU* 3.8 26.5 - - + -
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Residues in contact with VAL 49 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96H GLY 3.9 16.2 - - - +
97H PRO* 3.6 15.9 - - + +
99H PHE 4.4 2.9 - - - +
101H VAL* 3.6 30.7 - - + -
33L ALA 3.8 0.7 - - - -
34L ASN* 3.5 22.4 - - - +
46L GLY* 6.1 0.2 - - - -
47L LEU 6.0 0.2 - - - +
48L ILE* 1.3 79.5 - - - +
50L GLY* 1.3 67.1 + - - +
51L THR 3.2 2.7 - - - -
53L ASN* 2.9 46.6 + - + +
55L VAL* 4.4 11.2 - - + -
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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