Contacts of the strand formed by residues 3 - 8 (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 ILE 3 (chain 2).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12 THR* 3.6 16.8 - - + -
22 SER* 1.3 81.7 - - - +
42 MET* 1.3 63.8 + - - +
152 GLY 3.5 4.3 - - - +
162 ALA* 3.8 17.5 - - + -
332 LYS* 4.6 3.6 - - + -
442 CYS* 3.7 42.0 - - + +
452 ARG 4.0 4.3 - - - +
462 SER* 3.8 26.2 - - - +
982 GLY 4.4 1.3 - - - +
1002 ILE* 4.0 8.7 - - + +
1262 ILE* 3.3 2.4 - - - +
1272 ALA* 2.8 56.7 + - + +
1282 GLY 4.2 0.2 - - - +
1312 SER* 5.2 0.2 - - - -
1592 LEU* 4.5 1.7 - - - +
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Residues in contact with MET 4 (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* 1.3 75.8 - - - +
52 ALA* 1.3 58.8 + - - +
62 VAL* 3.7 11.0 - - + -
132 ILE 4.5 0.2 - - - -
142 LEU* 3.5 2.6 - - - -
152 GLY 2.8 35.5 + - - +
442 CYS* 4.1 4.9 - - - -
1002 ILE* 4.4 4.7 - - - -
1242 TYR* 4.6 2.5 - - + -
1252 ALA 3.2 12.6 - - - +
1262 ILE* 3.6 21.5 - - + -
1342 ILE* 4.8 0.9 - - - -
1382 CYS* 4.1 1.1 - - - -
1542 PHE* 3.7 32.8 - - + -
1552 ILE* 4.0 28.5 - - + -
1582 SER* 3.5 29.4 - - - +
1592 LEU* 3.9 20.6 - - + -
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Residues in contact with ALA 5 (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* 1.3 75.1 - - - +
62 VAL* 1.3 63.5 + - - +
132 ILE 3.2 9.2 - - - +
142 LEU* 4.5 5.8 - - + -
442 CYS* 5.3 0.4 - - - -
1002 ILE* 3.6 26.9 - - + +
1022 ALA* 4.2 12.1 - - + -
1102 VAL* 3.8 18.6 - - + +
1242 TYR* 3.1 6.1 - - - +
1252 ALA 2.9 31.4 + - - +
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Residues in contact with VAL 6 (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* 3.7 19.5 - - + -
52 ALA* 1.3 81.0 - - - +
72 THR* 1.3 71.5 + - - +
82 PHE* 3.7 4.3 + - - -
122 VAL* 3.3 5.2 - - - +
132 ILE 2.8 33.5 + - - -
1242 TYR* 3.9 5.6 - - + -
1422 PHE* 3.7 26.9 - - + -
1462 MET* 5.4 1.8 - - - -
1512 THR* 3.8 22.9 - - + +
1542 PHE* 3.8 11.4 - - + -
1552 ILE* 3.7 25.8 - - + -
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Residues in contact with THR 7 (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* 1.3 84.1 - - - +
82 PHE* 1.3 61.4 + - - +
112 GLY 3.4 8.5 - - - -
122 VAL* 4.0 2.4 - - + +
1082 GLY 3.7 28.3 - - - +
1092 GLU* 4.0 0.7 - - - -
1102 VAL* 3.7 25.5 - - + +
1212 LYS* 6.3 0.2 - - - +
1222 LEU 4.4 1.8 - - - +
1232 PRO* 2.6 35.9 + - + +
1422 PHE* 4.1 10.2 - - - -
1432 ARG 5.2 0.7 - - - +
1442 GLU* 5.2 4.2 + - - -
1452 ASN 5.1 2.5 + - - -
1462 MET* 5.4 1.2 + - - +
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Residues in contact with PHE 8 (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 3.9 5.8 - - - -
72 THR* 1.3 76.9 - - - +
92 LYS* 1.3 79.0 + - - +
102 ASP* 3.4 24.0 - - + -
112 GLY* 2.8 30.6 + - - +
122 VAL* 3.4 24.9 - - - -
132 ILE* 3.6 21.5 - - + -
1072 LYS* 4.6 5.5 - - - +
1082 GLY 5.3 0.5 + - - -
1452 ASN* 4.5 8.2 + - - +
1462 MET* 3.3 23.8 - - + +
1472 SER* 4.0 1.1 - - - -
1482 LYS* 3.8 32.5 - - + -
1512 THR* 3.3 22.7 - - - +
1772 VAL* 4.4 5.2 - - + -
1792 THR* 3.8 16.8 - - + -
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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