Contacts of the strand formed by residues 41 - 48 (chain L) in PDB entry 1OZT
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 GLY 41 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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39L THR 3.4 0.6 + - - -
40L GLU* 1.3 80.2 - - - +
42L LEU* 1.3 67.7 + - - -
43L HIS* 3.5 9.2 - - - -
88L THR* 3.3 6.4 - - - -
89L ALA 2.7 40.8 + - - -
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Residues in contact with LEU 42 (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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41L GLY* 1.3 72.9 - - - -
43L HIS* 1.3 69.3 + - - +
86L ASN* 3.9 26.2 - - + +
87L VAL 3.5 2.0 - - - +
88L THR* 3.1 32.8 - - + +
121L GLU 4.5 0.3 - - - +
122L LYS* 3.9 0.9 - - - -
123L ALA* 3.5 34.3 + - + +
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Residues in contact with HIS 43 (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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38L LEU* 3.4 24.0 - - + +
39L THR* 2.8 43.9 + - + -
41L GLY 3.5 23.1 + - - -
42L LEU* 1.3 76.7 + - - +
44L GLY* 1.3 63.8 + - - +
86L ASN* 3.1 6.0 + - - -
87L VAL* 2.8 41.8 + - + +
89L ALA* 4.4 1.8 - - + -
119L VAL* 3.9 13.7 - - + -
120L HIS 2.9 22.8 + - - +
121L GLU 3.0 20.2 + - - -
122L LYS 3.8 2.9 - - - -
144L LEU* 4.2 13.5 - - + +
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Residues in contact with GLY 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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43L HIS* 1.3 71.9 - - - +
45L PHE* 1.3 59.0 + - - -
46L ARG* 4.7 2.5 - - - -
85L GLY 3.6 2.9 - - - -
86L ASN* 3.4 12.0 + - - -
119L VAL* 3.3 4.3 - - - +
120L HIS* 2.6 43.0 + - - -
122L LYS 2.8 20.7 + - - -
124L ASP* 3.9 11.2 - - - -
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Residues in contact with PHE 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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8L LEU* 5.6 1.1 - - + -
18L ILE* 4.2 19.3 - - + -
20L PHE* 6.0 0.2 - + - -
31L VAL* 4.2 8.7 - - + -
35L ILE* 4.1 15.0 - - + -
43L HIS 4.1 2.7 - - - +
44L GLY* 1.3 72.7 - - - -
46L ARG* 1.3 64.6 + - - +
84L LEU* 3.1 56.6 + - + +
85L GLY 2.9 14.7 + - - +
86L ASN 4.2 3.4 - - - -
87L VAL* 3.5 34.1 - - + -
97L VAL* 4.3 1.6 - - + -
99L ILE* 4.0 21.1 - - + -
117L LEU* 3.8 33.2 - - + -
118L VAL 3.5 10.3 - - - -
119L VAL* 4.5 10.5 - - + -
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Residues in contact with ARG 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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44L GLY* 5.0 1.5 - - - -
45L PHE* 1.3 84.5 - - - +
47L VAL* 1.3 65.3 + - - +
48L HIS* 3.7 16.1 + - + +
63L HIS* 4.1 15.5 + - + +
82L GLY 3.2 11.0 - - - +
83L ASP* 3.3 24.3 + - - +
84L LEU* 4.4 1.8 - - - +
117L LEU* 3.4 6.3 - - - +
118L VAL* 2.6 41.4 + - - -
120L HIS* 3.4 36.8 + - - +
124L ASP* 3.0 42.9 + - - +
125L ASP* 3.6 15.8 + - - +
126L LEU 4.1 7.1 + - - -
138L GLY 3.1 25.8 + - - -
140L ALA* 4.2 4.9 - - - +
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Residues in contact with VAL 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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20L PHE* 5.3 0.4 - - + -
46L ARG* 1.3 76.2 - - - +
48L HIS* 1.3 63.5 + - - +
63L HIS* 3.4 4.9 - - - +
64L PHE* 2.6 34.7 + - + +
82L GLY* 2.9 23.0 + - - +
84L LEU* 4.1 22.4 - - + -
104L ILE* 4.8 2.0 - - + -
112L ILE* 4.0 37.0 - - + -
115L ARG* 4.0 12.3 - - + -
116L THR 3.2 10.3 - - - +
117L LEU* 4.2 9.4 - - + -
149L ILE* 4.3 11.2 - - + -
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Residues in contact with HIS 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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46L ARG* 3.7 13.3 - - + +
47L VAL* 1.3 82.8 - - - +
49L GLU* 1.3 65.0 + - - +
50L PHE 3.4 0.4 - - - -
60L ALA* 3.5 22.9 - - + +
61L GLY 2.9 18.5 + - - +
62L PRO 3.2 11.7 - - - +
63L HIS* 4.0 12.1 - - + -
64L PHE* 3.8 2.2 - - - -
115L ARG* 3.4 8.3 - - - +
116L THR 2.7 26.1 + - - +
118L VAL* 3.2 25.9 - - + +
120L HIS* 3.0 35.8 + + - -
143L ARG* 3.5 22.2 + - - -
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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