Contacts of the strand formed by residues 77 - 82 (chain D) in PDB entry 1SL0
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 THR 77 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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27D PHE* 3.4 33.6 + - + -
72D ILE* 3.3 28.7 - - + +
73D ARG 4.6 0.9 + - - -
74D GLY 2.3 34.4 + - - -
75D ILE* 3.1 7.9 - - - +
76D PRO* 1.3 69.4 - - - +
78D LEU* 1.3 60.2 + - - +
79D LEU* 3.2 26.2 - - + -
89D THR* 5.4 3.6 - - - -
90D LYS 4.0 3.6 - - - -
91D VAL* 3.8 19.4 - - + +
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Residues in contact with LEU 78 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24D LEU* 4.0 20.9 - - + -
25D VAL 3.7 2.5 - - - +
26D ASP* 3.5 33.7 - - + +
38D ILE* 3.3 30.7 - - + -
42D LEU* 4.6 4.9 - - + -
76D PRO 3.2 16.6 - - - +
77D THR* 1.3 71.7 - - - +
79D LEU* 1.3 65.0 + - - +
88D ALA 3.6 0.5 - - - +
89D THR* 3.1 6.9 - - - -
90D LYS* 2.8 48.3 + - + +
92D GLY 4.2 2.0 - - - +
94D LEU* 3.8 27.4 - - + -
99D LEU* 6.2 1.6 - - + -
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Residues in contact with LEU 79 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23D ILE 3.6 0.2 - - - +
24D LEU* 3.1 7.0 - - - +
25D VAL* 2.7 39.5 + - + +
27D PHE* 4.0 9.9 - - + -
70D TYR* 3.8 26.2 - - + -
72D ILE* 4.7 1.1 - - + -
77D THR* 3.2 30.3 - - + +
78D LEU* 1.3 83.7 - - - +
80D LEU* 1.3 59.1 + - - +
81D PHE* 3.4 28.8 + - + -
86D VAL* 3.2 31.6 - - + -
88D ALA 3.2 3.6 - - - -
89D THR* 3.7 14.6 - - + -
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Residues in contact with LEU 80 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22D ALA* 6.3 2.2 - - + -
23D ILE 3.7 4.0 - - - -
24D LEU* 4.0 14.6 - - + +
53D LEU* 6.1 2.9 - - + -
79D LEU* 1.3 72.1 - - - +
81D PHE* 1.3 56.8 + - - +
87D ALA* 2.7 44.3 + - + +
88D ALA* 3.0 22.7 + - + +
106D ASN* 5.6 8.1 - - + +
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Residues in contact with PHE 81 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12D PHE* 4.1 10.5 - + - -
16D VAL* 4.1 22.2 - - + +
17D LEU* 4.5 10.1 - - + -
21D GLY 3.9 1.2 - - - +
22D ALA* 3.2 9.9 - - - +
23D ILE* 2.6 39.3 + - + +
25D VAL* 3.1 29.6 - - + -
70D TYR* 3.3 44.4 - + - -
79D LEU* 3.4 35.4 - - + -
80D LEU* 1.3 73.9 - - - +
82D LYS* 1.3 59.9 + - - +
83D ASN 3.9 1.6 - - - +
84D GLY 4.4 15.3 - - - -
85D GLU 4.0 15.3 - - - -
86D VAL* 3.8 9.9 - - + -
87D ALA 4.4 0.4 - - - +
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Residues in contact with LYS 82 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20D ASP 5.7 0.2 - - - -
21D GLY 4.4 5.6 - - - -
22D ALA* 4.9 6.7 - - + +
80D LEU 3.6 1.4 + - - -
81D PHE* 1.3 76.9 - - - +
83D ASN* 1.3 70.9 - - - +
85D GLU 3.5 10.6 + - - +
87D ALA* 3.7 20.2 - - + -
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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