Contacts of the strand formed by residues 34 - 39 (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 ASN 34 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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97H PRO 2.9 23.6 + - - -
98H GLY* 3.4 3.5 - - - -
99H PHE* 2.8 39.5 + - + +
32L TYR 2.9 18.4 + - - -
33L ALA* 1.3 74.6 - - - +
35L TRP* 1.3 66.2 + - - +
36L VAL* 4.9 4.9 - - + +
48L ILE 3.2 3.6 - - - +
49L VAL* 3.5 18.5 - - - +
88L CYS* 3.1 10.1 - - - +
89L ALA* 2.9 43.2 + - + +
96L TRP* 3.6 6.5 - - - -
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Residues in contact with TRP 35 (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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6L GLN* 3.6 22.0 - - - -
21L LEU* 3.8 26.2 - - + -
22L THR 3.8 6.7 - - - -
23L CYS* 3.7 30.7 - - + -
33L ALA* 4.7 6.1 - - - +
34L ASN* 1.3 78.9 + - - +
36L VAL* 1.3 64.7 + - - +
47L LEU* 2.9 28.6 + - + +
48L ILE* 2.9 36.1 + - + +
51L THR 5.0 2.3 + - - -
64L GLY* 5.0 0.4 - - - -
65L SER 5.3 0.2 + - - -
71L ALA* 3.8 8.3 - - + +
72L ALA* 3.6 25.0 + - - +
73L LEU* 3.4 57.2 - - + -
86L TYR* 4.7 4.5 - - + -
87L PHE 3.4 10.8 - - - -
88L CYS* 3.8 11.4 - - + -
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Residues in contact with VAL 36 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45H LEU* 4.7 3.4 - - + -
99H PHE* 3.9 15.7 - - + +
103H TRP* 3.8 35.0 - - + +
34L ASN* 4.9 7.0 - - + +
35L TRP* 1.3 83.0 - - - +
37L GLN* 1.3 60.1 + - - +
44L PHE* 4.0 21.5 - - + -
45L THR 3.4 9.9 - - - +
46L GLY* 4.2 2.7 - - - -
47L LEU* 4.2 4.0 - - - +
48L ILE 5.6 0.2 - - - +
86L TYR* 3.4 5.5 - - - +
87L PHE* 2.8 55.9 + - + +
88L CYS 6.1 0.2 - - - -
89L ALA* 6.3 0.4 - - + -
98L PHE* 4.9 4.7 - - + -
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Residues in contact with GLN 37 (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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36L VAL* 1.3 73.6 - - - +
38L GLU* 1.3 59.5 + - - +
39L LYS* 3.8 26.0 - - - +
43L LEU 3.3 2.1 - - - +
44L PHE* 3.2 8.2 - - - -
45L THR* 2.9 51.6 + - - +
47L LEU* 3.8 21.1 - - + +
62L PHE* 4.3 11.9 - - - -
81L GLU 4.4 4.8 + - - -
82L ASP* 4.4 1.2 + - - +
84L ALA* 3.4 26.7 - - + +
85L ILE 3.5 3.6 - - - -
86L TYR* 2.9 31.1 + - + -
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Residues in contact with GLU 38 (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* 3.9 13.8 + - - -
36L VAL 4.3 0.2 + - - -
37L GLN* 1.3 74.1 - - - +
39L LYS* 1.3 71.9 + - - +
41L ASP* 5.0 2.9 - - - +
42L HIS* 3.5 23.4 + - - +
43L LEU 3.3 2.9 - - - -
44L PHE* 3.5 35.2 - - + -
84L ALA* 3.3 6.0 - - - +
85L ILE* 2.7 54.5 + - + +
87L PHE* 3.4 22.2 - - + -
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Residues in contact with LYS 39 (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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37L GLN* 3.8 27.6 - - - +
38L GLU* 1.3 78.0 - - - +
40L PRO* 1.3 78.3 - - + +
42L HIS 3.3 5.4 + - - -
43L LEU* 2.9 51.8 + - + +
81L GLU* 3.1 37.2 + - - +
83L GLU 3.6 19.7 + - - +
84L ALA* 3.9 4.9 - - + +
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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