Contacts of the strand formed by residues 69 - 75 (chain A) in PDB entry 3L43
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 69 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48A LEU* 4.9 0.2 - - + -
56A PHE* 4.6 2.7 - - + -
57A LEU* 3.8 29.4 - - + -
65A THR* 5.9 1.1 - - + -
67A ARG 3.5 3.5 + - - +
68A PRO* 1.3 71.9 - - - +
70A VAL* 1.3 63.1 + - - +
71A LEU* 3.3 20.8 + - + +
101A ILE* 4.4 17.0 - - + -
120A ILE* 3.4 36.8 - - + +
122A LEU* 3.9 27.8 - - + -
134A LEU 3.4 0.2 - - - +
135A ILE* 3.3 4.7 - - - -
136A ASP* 2.8 51.3 + - + +
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Residues in contact with VAL 70 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A GLN* 4.0 10.5 - - - +
68A PRO 4.0 0.2 + - - -
69A LEU* 1.3 69.9 - - - +
71A LEU* 1.3 58.1 + - - +
72A GLN* 3.7 2.8 + - + +
119A PRO* 4.1 22.4 - - + -
120A ILE 2.8 10.1 + - - +
121A ASN* 3.5 26.4 - - - +
122A LEU 2.9 30.1 + - - +
133A THR* 3.8 24.7 - - + -
134A LEU 3.7 3.4 - - - +
135A ILE* 4.1 16.8 - - + +
163A PHE* 4.2 13.0 - - + -
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Residues in contact with LEU 71 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A LEU* 3.8 29.6 - - + +
52A VAL* 4.2 3.8 - - + -
56A PHE* 3.6 25.8 - - + -
69A LEU* 4.3 12.1 - - + +
70A VAL* 1.3 70.6 - - - +
72A GLN* 1.4 59.7 + - - +
73A LEU* 3.8 27.5 + - + +
122A LEU* 3.4 33.7 - - + +
124A VAL* 4.0 13.5 - - + -
132A LEU 3.7 1.7 - - - +
133A THR* 3.5 2.7 - - - -
134A LEU* 2.7 47.5 + - + +
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Residues in contact with GLN 72 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70A VAL* 3.7 4.3 + - + +
71A LEU* 1.4 72.4 - - - +
73A LEU* 1.3 67.7 + - - +
74A ILE* 3.7 26.5 - - + +
122A LEU 2.8 9.5 + - - +
123A ARG* 3.3 25.4 - - + +
124A VAL 2.9 27.4 + - - +
132A LEU 3.7 2.5 - - - +
133A THR* 3.4 26.0 + - + +
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Residues in contact with LEU 73 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51A PHE* 3.8 32.8 - - + +
52A VAL* 3.7 23.6 - - + -
71A LEU* 3.8 22.7 - - + +
72A GLN* 1.3 77.9 + - - +
74A ILE* 1.3 62.9 + - - +
124A VAL* 3.5 13.0 - - + +
129A VAL* 3.9 14.6 - - + -
130A LEU 3.2 25.9 - - - +
131A ASN* 3.4 4.7 - - - +
132A LEU* 2.8 29.4 + - + +
134A LEU* 3.8 26.2 - - + -
278A GLN* 6.1 0.4 - - - +
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Residues in contact with ILE 74 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72A GLN* 3.7 37.0 - - + +
73A LEU* 1.3 78.9 - - - +
75A THR* 1.4 75.3 + - - +
76A SER* 5.0 0.2 - - - -
123A ARG* 4.0 17.0 - - + -
124A VAL 2.9 8.9 + - - +
125A TYR* 3.2 48.9 - - + +
126A SER 2.9 25.1 + - - -
129A VAL* 3.5 4.2 - - - +
131A ASN* 3.5 8.7 - - - +
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Residues in contact with THR 75 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74A ILE* 1.4 78.7 - - - +
76A SER* 1.4 62.8 + - - +
126A SER 3.4 9.6 - - - +
127A PRO* 4.3 11.7 - - + +
129A VAL* 2.7 28.3 + - - +
130A LEU* 3.6 9.9 + - - +
131A ASN* 3.0 23.0 + - - +
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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