Contacts of the strand formed by residues 59 - 66 (chain 0) in PDB entry 5IY8
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 ARG 59 (chain 0).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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570 MET* 3.9 13.7 - - - +
580 MET* 1.4 80.5 - - - +
600 HIS* 1.3 58.1 + - - +
610 LEU* 5.2 3.4 - - - +
950 TYR* 3.5 28.0 - - - +
990 ASN* 3.5 28.1 - - + +
1010 ILE 3.6 4.6 + - - +
1020 SER* 3.2 5.1 - - - -
1030 GLN* 2.7 36.7 + - - -
1640 SER* 3.4 14.6 - - - +
1660 GLU* 2.9 37.1 + - - +
2350 HIS* 3.2 20.2 + - - +
2360 VAL 3.1 17.8 + - - -
2370 SER 3.1 26.2 + - - -
2380 PRO* 3.7 0.8 - - - +
2390 PRO* 3.8 15.8 - - + +
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Residues in contact with HIS 60 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
580 MET* 4.0 14.4 - - + +
590 ARG* 1.3 77.2 - - - +
610 LEU* 1.3 58.8 + - - +
620 TYR 4.4 0.2 - - - -
1030 GLN* 3.2 44.3 + - + +
1200 LEU* 3.8 5.3 - - + +
1560 LEU* 4.4 18.2 - - + +
1590 MET* 3.1 49.7 - - + +
1600 PRO* 4.7 1.8 - - - +
1630 THR* 3.6 25.6 + - - +
1640 SER* 3.4 14.1 + - - +
1660 GLU* 3.0 28.0 + - - +
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Residues in contact with LEU 61 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
590 ARG* 5.2 3.1 - - - +
600 HIS* 1.3 72.2 - - - +
620 TYR* 1.3 63.4 + - - +
630 VAL* 4.3 7.9 - - + -
910 PHE* 3.8 24.7 - - + -
950 TYR* 3.5 39.0 - - + +
1030 GLN 3.0 7.9 + - - +
1040 ILE* 3.1 34.2 - - + +
1050 GLY 3.1 3.3 + - - -
1200 LEU* 5.1 1.0 - - - +
1660 GLU* 3.4 30.3 - - + +
1670 VAL 4.4 0.4 - - - -
1680 LEU* 3.8 27.1 - - + +
2350 HIS* 5.8 1.8 - - + +
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Residues in contact with TYR 62 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
610 LEU* 1.3 70.3 - - - +
630 VAL* 1.3 64.4 + - - +
640 VAL* 3.4 3.5 + - + +
1050 GLY* 3.4 24.0 - - - -
1060 ILE 4.5 1.1 - - - -
1070 ILE* 3.7 38.1 - - + -
1160 LYS* 6.1 2.1 - - + +
1180 THR 5.1 2.4 + - - -
1190 GLU* 5.1 1.7 - - - -
1200 LEU* 3.7 34.4 + - + +
1510 ILE* 5.1 4.1 - - + +
1520 ALA* 4.1 22.9 - - + -
1550 THR* 2.9 43.0 + - - +
1560 LEU* 3.4 20.4 - - + -
1660 GLU 2.7 15.3 + - - +
1670 VAL* 3.4 10.6 - - + +
1680 LEU 3.0 23.5 + - - +
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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
----------------------------------------------------------
610 LEU* 4.3 11.0 - - + -
620 TYR* 1.3 71.6 - - - +
640 VAL* 1.3 63.3 + - - +
650 VAL* 5.5 1.6 - - + -
880 LEU* 4.1 31.2 - - + -
910 PHE* 4.3 20.9 - - + -
920 VAL* 6.1 2.5 - - + -
1040 ILE* 3.7 23.6 - - + -
1050 GLY 3.0 7.8 + - - +
1060 ILE* 3.4 20.3 - - + +
1070 ILE* 3.0 27.1 + - - +
1310 LEU* 5.9 3.1 - - + -
1680 LEU* 3.6 9.6 - - + +
1700 ILE* 4.2 11.2 - - + -
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Residues in contact with VAL 64 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
620 TYR* 3.8 6.3 - - + +
630 VAL* 1.3 75.6 - - - +
650 VAL* 1.3 66.6 + - - +
1070 ILE* 3.3 22.7 - - + +
1090 THR* 4.7 9.4 - - + +
1450 LEU* 5.0 5.6 - - + -
1480 SER* 4.5 23.1 - - - +
1490 LEU* 5.6 1.6 - - + -
1520 ALA* 5.6 1.1 - - + -
1670 VAL* 3.8 26.7 - - + -
1680 LEU 2.8 10.0 + - - +
1690 ILE* 3.4 27.3 - - + -
1700 ILE* 3.1 27.1 + - - +
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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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630 VAL* 5.5 1.3 - - + -
640 VAL* 1.3 78.1 - - - +
660 ASP* 1.3 74.5 + - - +
670 GLY* 3.3 1.3 + - - +
710 MET* 4.1 15.0 - - + -
810 LEU* 5.3 5.2 - - + -
840 THR* 4.7 2.7 - - - +
850 LEU* 4.5 24.2 - - + -
880 LEU* 4.6 18.6 - - + -
1060 ILE* 5.0 6.5 - - + -
1070 ILE 3.1 18.0 + - - +
1080 VAL* 3.5 17.9 - - + +
1090 THR* 3.0 27.8 + - - -
1170 LEU* 4.5 12.1 - - + -
1310 LEU* 5.7 1.3 - - + -
1690 ILE* 6.1 0.2 - - - -
1700 ILE* 3.9 5.8 - - + +
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Residues in contact with ASP 66 (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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650 VAL* 1.3 77.5 - - - +
670 GLY* 1.3 56.3 + - - +
680 SER* 2.6 28.5 + - - -
700 THR* 4.0 1.8 + - - -
710 MET* 3.1 32.9 - - + +
810 LEU* 4.9 0.3 - - - +
1090 THR* 3.8 12.4 + - - +
1430 PRO* 4.2 2.8 - - - +
1450 LEU* 6.6 0.4 - - + -
1700 ILE 3.0 22.1 + - - +
1710 PHE* 4.1 4.5 - - + -
1720 SER* 3.1 30.3 + - - +
1730 SER* 2.6 28.0 + - - -
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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
------------------------------------------------------------
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