Contacts of the strand formed by residues 60 - 66 (chain 0) in PDB entry 5OA3
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 ALA 60 (chain 0).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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520 LYS* 5.1 13.7 - - + -
530 LEU 3.5 8.1 - - - +
540 TYR* 4.6 16.1 - - + -
580 GLY 4.2 1.4 + - - -
590 ASP* 1.3 71.4 - - - +
610 VAL* 1.3 60.5 + - - +
620 THR* 4.2 6.4 + - + +
740 GLU 4.4 0.2 - - - +
750 LEU* 3.7 18.6 - - - +
760 GLU* 4.5 17.1 + - + +
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Residues in contact with VAL 61 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10 MET* 4.5 19.1 - - + +
20 PHE* 3.8 32.3 - - + -
60 PHE* 5.7 4.7 - - + -
510 VAL 3.6 0.2 - - - +
520 LYS* 3.7 0.7 - - - +
530 LEU* 2.9 50.7 + - + -
550 ALA* 4.9 8.7 - - + +
590 ASP* 4.1 10.3 - - + +
600 ALA* 1.3 73.9 - - - +
620 THR* 1.3 74.3 + - - +
630 VAL* 4.7 0.4 - - + -
740 GLU 3.8 12.3 - - - +
750 LEU* 3.8 19.3 - - + -
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Residues in contact with THR 62 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
500 ILE* 3.9 28.4 - - + +
510 VAL 3.3 4.3 - - - +
520 LYS* 4.7 11.7 - - + -
600 ALA* 4.8 6.5 - - + +
610 VAL* 1.3 79.9 - - - +
630 VAL* 1.3 64.0 + - - +
640 TYR* 3.9 1.4 + - - +
730 PHE* 3.2 3.5 - - - -
740 GLU* 3.0 60.4 + - + +
790 LEU* 5.5 0.7 - - - +
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Residues in contact with VAL 63 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20 PHE* 4.5 3.4 - - + -
500 ILE* 4.5 0.9 - - - -
510 VAL* 2.9 49.3 + - + +
530 LEU* 4.0 24.5 - - + -
610 VAL* 4.7 0.4 - - + -
620 THR* 1.3 74.5 - - - +
640 TYR* 1.3 63.3 + - - +
650 VAL* 3.5 18.2 + - + +
700 PRO* 4.0 19.5 - - + -
720 LEU 3.7 9.2 - - - +
730 PHE* 3.9 15.5 - - + -
820 THR* 5.3 0.7 - - + -
1760 LEU* 4.1 19.7 - - + -
1820 LYS* 4.7 8.1 - - - -
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Residues in contact with TYR 64 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140 ILE* 4.4 4.5 - - + -
190 ARG 5.7 0.2 + - - -
220 LEU* 3.8 35.1 - - + +
230 ARG* 5.0 4.6 - - + +
260 VAL* 6.1 2.5 - - + -
420 VAL* 3.2 23.3 - - + +
480 LEU* 3.0 38.0 - - + +
490 ASN 3.8 6.7 - - - -
500 ILE* 4.2 15.9 - - + +
620 THR 3.9 2.6 + - - +
630 VAL* 1.3 71.9 - - - +
650 VAL* 1.3 60.6 + - - +
660 SER* 5.2 2.2 - - - -
700 PRO* 3.8 0.3 - - - +
710 ILE* 2.9 64.6 + - + -
720 LEU* 2.9 30.9 + - + +
790 LEU* 5.2 10.1 - - + -
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Residues in contact with VAL 65 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110 ASN* 5.8 0.9 - - - +
480 LEU* 3.9 0.5 - - - -
490 ASN* 2.9 52.4 + - + +
510 VAL* 4.0 6.3 - - + -
630 VAL* 3.6 14.6 - - + +
640 TYR* 1.3 81.3 - - - +
660 SER* 1.3 64.1 + - - +
670 GLY 4.8 0.2 - - - +
680 GLY* 3.9 25.8 - - - +
690 ASN 3.6 9.0 - - - +
700 PRO* 3.7 16.4 - - + -
710 ILE* 4.9 1.1 - - - -
1820 LYS* 3.6 35.7 - - + +
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Residues in contact with SER 66 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
410 LEU* 4.1 13.1 + - - +
420 VAL* 4.9 2.5 - - - -
430 PRO* 4.1 6.4 - - - +
460 GLU* 3.7 17.1 + - - +
470 GLU 3.3 19.9 + - - -
480 LEU* 4.4 14.4 - - - +
490 ASN* 5.4 0.9 - - - +
640 TYR* 5.2 1.8 - - - -
650 VAL* 1.3 74.2 - - - +
670 GLY* 1.3 64.4 + - - +
680 GLY 3.3 1.6 + - - -
690 ASN* 3.6 21.1 + - - +
710 ILE* 4.1 18.8 - - - +
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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