Contacts of the strand formed by residues 33 - 38 (chain L) in PDB entry 4ZFO
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 VAL 33 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4L MET* 4.1 8.7 - - + -
29L VAL* 3.6 12.1 - - + -
31L SER 2.9 7.5 + - - +
32L ASN* 1.3 79.9 - - - +
34L ALA* 1.3 70.3 + - - +
35L TRP* 4.1 18.6 - - - +
48L ILE* 4.5 0.9 - - - +
49L PHE 3.6 1.0 - - - -
50L SER 3.3 6.4 + - - -
51L ALA* 2.8 28.4 + - - -
71L PHE* 3.6 52.3 - - + -
88L CYS* 4.7 5.6 - - + -
89L GLN 3.2 14.8 - - - +
90L GLN* 4.5 0.4 - - - -
91L TYR* 3.6 3.7 - - - -
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Residues in contact with ALA 34 (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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17K LEU* 3.7 26.9 - - + -
33L VAL* 1.3 76.9 - - - +
35L TRP* 1.3 65.8 + - - +
36L TYR* 3.8 20.6 - - + -
48L ILE 3.1 16.4 - - - +
55L PHE* 5.4 0.4 - - + -
88L CYS* 3.4 4.0 - - - -
89L GLN* 2.9 36.8 + - - +
91L TYR* 3.8 3.5 - - + -
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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* 4.3 4.9 - - - -
21L VAL* 3.4 39.3 - - + -
23L CYS* 3.6 29.8 - - + -
33L VAL* 4.1 12.2 - - + +
34L ALA* 1.3 76.3 - - - +
36L TYR* 1.3 61.4 + - - +
46L ALA* 3.8 1.2 - - - +
47L LEU* 2.8 33.9 + - + -
48L ILE* 3.0 40.7 + - + +
51L ALA* 4.7 5.7 + - - +
64L GLY* 5.2 0.2 - - - -
65L SER 5.4 0.2 + - - -
71L PHE* 4.1 5.7 - - + +
72L THR 3.8 14.6 + - - -
73L LEU* 3.5 52.2 - - + +
86L TYR* 4.7 2.0 - - + -
87L PHE 3.3 23.1 - - - -
88L CYS* 3.7 19.7 - - + -
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Residues in contact with TYR 36 (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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45H LEU* 4.6 9.4 - - + -
99H LEU* 3.6 22.4 - - + +
110H TRP* 3.7 38.4 - + - -
17K LEU* 3.7 6.4 - - + +
34L ALA* 3.8 12.8 - - + -
35L TRP* 1.3 77.8 - - - +
37L GLN* 1.3 63.2 + - - +
44L PRO* 4.8 2.5 - - + -
45L LYS 3.3 7.2 - - - +
46L ALA* 3.9 19.3 - - + -
47L LEU* 4.0 5.1 - - - +
55L PHE* 6.1 0.2 - + - -
86L TYR* 3.3 8.7 - - - +
87L PHE* 2.8 45.6 + - + +
89L GLN* 2.5 48.4 + - + -
98L PHE* 3.7 18.6 - + - -
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Residues in contact with GLN 37 (chain L).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36L TYR* 1.3 75.4 - - - +
38L GLN* 1.3 66.6 + - - +
39L LYS* 4.0 17.7 + - + +
43L SER 4.3 0.3 - - - +
44L PRO* 3.2 5.0 - - - +
45L LYS* 2.8 65.7 + - + +
47L LEU* 3.9 13.1 - - + +
62L PHE* 4.3 9.5 - - - -
81L GLU 4.2 11.9 + - - -
82L ASP* 4.3 3.6 + - - +
84L ALA* 3.9 15.2 - - + +
85L GLU 3.4 4.3 - - - +
86L TYR* 2.9 40.4 + - + -
87L PHE* 5.3 0.9 - - - -
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Residues in contact with GLN 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 ARG* 2.8 36.5 + - - +
45H LEU* 3.3 18.3 - - + +
95H TYR* 3.2 23.2 + - - -
37L GLN* 1.3 78.2 - - - +
39L LYS* 1.3 73.1 + - - +
40L PRO* 4.8 0.7 - - - +
42L GLN 2.8 25.9 + - - +
43L SER 4.0 7.6 - - - +
44L PRO* 3.6 23.3 - - + +
84L ALA* 3.5 0.7 - - - +
85L GLU* 2.8 37.0 + - - +
87L PHE* 4.4 9.6 - - + -
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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