Contacts of the strand formed by residues 44 - 51 (chain 1) in PDB entry 1SVA
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 PHE 44 (chain 1).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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241 PRO* 3.9 32.5 - - + -
421 ASP 4.3 7.6 - - - +
431 SER* 1.3 81.8 + - - +
451 THR* 1.3 71.6 + - - +
461 GLU* 4.1 22.2 - - + -
1101 TRP* 5.4 0.2 - - - -
2891 THR* 4.4 17.3 - - + -
2901 LEU 3.4 14.6 - - - +
2911 ARG* 4.5 9.0 - - + +
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Residues in contact with THR 45 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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351 LEU* 4.4 17.9 - - + +
391 THR* 5.4 5.8 - - + +
431 SER* 3.9 7.2 - - - +
441 PHE* 1.3 85.4 - - - +
461 GLU* 1.3 64.7 + - - +
471 VAL* 4.0 15.2 - - - +
1101 TRP* 3.8 30.7 - - + -
2881 ILE 3.6 1.4 - - - +
2891 THR* 3.4 1.8 - - - -
2901 LEU* 2.8 40.2 + - - +
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Residues in contact with GLU 46 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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441 PHE* 4.1 20.4 - - + +
451 THR* 1.3 80.5 + - - +
471 VAL* 1.3 63.9 + - - +
481 GLU* 4.0 10.0 + - + +
2871 LYS* 3.0 43.0 + - + -
2881 ILE 3.3 6.7 - - - +
2891 THR* 4.2 16.8 - - + +
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Residues in contact with VAL 47 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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321 ILE* 5.4 7.0 - - + -
351 LEU* 4.9 17.3 - - + -
451 THR* 4.0 14.1 - - - +
461 GLU* 1.3 77.3 - - - +
481 GLU* 1.3 69.6 + - - +
491 CYS* 4.6 1.5 - - + -
931 ILE* 3.9 37.0 - - + -
951 LEU* 5.6 0.4 - - + -
2591 LEU* 5.2 1.8 - - + -
2861 PHE 3.2 2.6 - - - +
2871 LYS* 3.2 2.5 - - - -
2881 ILE* 2.8 41.5 + - + +
2901 LEU* 4.1 18.2 - - + -
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Residues in contact with GLU 48 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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461 GLU* 4.0 9.8 + - + +
471 VAL* 1.3 79.4 - - - +
491 CYS* 1.3 64.6 + - - +
2851 TYR* 2.8 34.6 + - + +
2861 PHE 3.1 6.5 - - - +
2871 LYS* 3.9 23.8 + - + +
2132 SER* 2.4 35.2 - - - +
2162 GLU* 2.9 20.6 - - - +
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Residues in contact with CYS 49 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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471 VAL* 4.6 4.5 - - + -
481 GLU* 1.3 77.6 - - - +
501 PHE* 1.3 83.8 + - + +
511 LEU* 6.1 0.7 - - - -
931 ILE* 3.7 31.9 - - + -
2611 VAL* 5.3 5.8 - - - -
2851 TYR* 3.4 7.5 - - - +
2861 PHE* 2.9 44.6 + - - -
2881 ILE* 5.0 1.3 - - - -
2132 SER* 6.2 0.2 - - - -
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Residues in contact with PHE 50 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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491 CYS* 1.3 96.3 - - - +
511 LEU* 1.3 86.5 - - - +
521 ASN* 3.6 18.6 - - - -
1201 ILE* 5.0 3.8 - - + -
2831 PRO* 4.7 1.1 - - + -
2841 ARG 3.0 19.1 - - - +
2851 TYR* 4.0 3.4 - - + +
2861 PHE* 4.3 2.7 - - - -
1892 MET* 3.2 54.5 - - + -
1912 THR* 5.1 10.1 - - + -
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Residues in contact with LEU 51 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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491 CYS* 6.1 0.9 - - - -
501 PHE* 1.3 92.1 - - - +
521 ASN* 1.3 65.0 - - - +
891 SER* 3.5 31.9 - - - +
901 VAL 4.1 5.2 - - - +
911 ALA* 3.6 29.6 - - + -
2001 ASP* 5.5 0.9 - - - +
2611 VAL* 3.5 39.0 - - + +
2621 SER 4.2 0.2 - - - -
2631 ALA* 4.0 15.3 - - + +
2831 PRO* 3.0 7.1 - - - +
2841 ARG* 2.9 32.7 + - + +
2861 PHE* 4.4 3.1 - - + -
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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