Contacts of the strand formed by residues 11 - 17 (chain 2) in PDB entry 3SDI
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 11 (chain 2).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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72 THR* 3.4 3.3 - - - -
82 PHE* 2.8 39.1 + - - +
92 LYS 3.7 0.2 + - - -
102 ASP* 1.3 80.3 - - - +
122 VAL* 1.3 62.7 + - - +
1042 TYR* 3.9 11.4 - - - -
1082 GLY* 3.7 14.6 - - - -
1782 LEU 3.3 11.2 - - - -
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Residues in contact with VAL 12 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62 VAL 3.3 18.6 - - - +
72 THR* 4.0 2.7 - - - +
82 PHE* 3.4 3.2 - - - -
112 GLY* 1.3 76.6 - - - +
132 ILE* 1.3 71.5 + - - +
142 LEU* 4.9 0.2 - - + -
1022 ALA* 3.8 10.5 - - + -
1032 GLY 3.8 31.6 - - - +
1082 GLY* 4.3 5.2 - - - -
1092 GLU 4.4 0.9 - - - +
1102 VAL* 3.6 31.2 - - + -
1762 VAL 3.8 0.5 - - - +
1782 LEU* 3.0 52.3 + - + +
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Residues in contact with ILE 13 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52 ALA* 3.2 2.6 - - - -
62 VAL 2.8 37.3 + - - -
82 PHE* 3.6 17.5 - - + -
122 VAL* 1.3 79.9 - - - +
142 LEU* 1.3 73.6 + - - +
1482 LYS* 4.3 5.2 - - + +
1512 THR* 3.9 21.1 - - + -
1522 VAL* 3.8 28.3 - - + +
1552 ILE* 3.7 19.6 - - + +
1752 MET* 3.8 19.5 - - + -
1762 VAL 3.3 13.0 - - - +
1772 VAL* 3.9 20.6 - - + -
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Residues in contact with LEU 14 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42 MET 3.5 4.5 - - - -
52 ALA* 4.5 3.1 - - + -
122 VAL* 4.9 1.1 - - + -
132 ILE* 1.3 77.8 - - - +
152 GLY* 1.3 57.6 + - - +
342 LEU* 3.8 15.9 - - + +
422 TRP* 3.6 28.9 - - + +
432 CYS* 3.8 14.6 - - - +
442 CYS* 3.5 24.9 - - - -
1002 ILE 5.0 0.7 - - - +
1022 ALA* 3.7 28.0 - - + -
1552 ILE* 5.0 0.2 - - - -
1752 MET* 3.0 6.8 - - - +
1762 VAL* 2.7 46.9 + - + +
1782 LEU* 3.9 23.8 - - + -
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Residues in contact with GLY 15 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32 ILE* 3.5 2.3 - - - +
42 MET* 2.8 34.2 + - - +
132 ILE 4.1 0.6 + - - -
142 LEU* 1.3 73.4 - - - +
162 ALA* 1.3 64.5 + - - +
342 LEU* 4.0 4.3 - - - +
442 CYS* 4.2 0.3 - - - -
1552 ILE* 4.1 14.1 - - - +
1592 LEU* 3.7 15.3 - - - -
1742 ARG 3.0 9.4 - - - -
1752 MET* 4.2 1.1 - - - -
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Residues in contact with ALA 16 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22 SER 3.3 7.2 - - - -
32 ILE* 3.8 20.6 - - + -
152 GLY* 1.3 76.3 - - - +
172 ASP* 1.3 70.6 + - - +
332 LYS* 3.8 12.8 - - + +
342 LEU* 3.8 18.6 - - + -
1592 LEU* 3.5 9.3 - - - +
1732 ILE* 3.6 1.4 - - - -
1742 ARG* 2.9 33.9 + - + +
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Residues in contact with ASP 17 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22 SER* 2.8 38.1 + - - +
162 ALA* 1.3 80.3 - - - +
182 SER* 1.3 58.9 + - - +
192 ARG* 3.1 15.9 + - - +
312 THR 4.7 1.0 - - - +
332 LYS* 2.9 40.2 + - - +
1592 LEU* 4.3 2.6 - - + +
1632 ILE* 3.8 23.1 - - + -
1692 SER* 3.3 8.4 - - - -
1702 GLY 3.1 28.9 + - - +
1722 VAL 3.4 8.7 - - - -
1732 ILE* 4.7 0.9 - - - +
1742 ARG* 5.5 1.8 - - - +
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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