Contacts of the strand formed by residues 61 - 66 (chain 6) in PDB entry 4UOW
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 LEU 61 (chain 6).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256 ALA* 4.5 11.2 - - + -
266 CYS 3.4 26.0 - - - +
276 ALA* 4.0 1.6 - - - +
286 PHE* 3.3 10.0 - - - -
566 GLU 3.8 2.4 - - - +
576 ASN* 3.5 1.9 - - - -
586 THR* 2.8 49.3 + - + +
606 ASP* 1.3 80.7 - - - +
626 THR* 1.3 60.5 + - - +
636 THR* 3.3 25.1 - - - +
157 ARG* 3.9 32.3 - - + -
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Residues in contact with THR 62 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246 VAL 3.6 1.2 - - - +
256 ALA* 3.5 0.2 - - - -
266 CYS* 2.8 52.1 + - + +
286 PHE* 3.6 13.7 - - + -
366 VAL* 3.4 9.0 - - + +
386 TRP* 2.8 27.0 + - + +
556 ILE* 4.0 0.2 - - - +
566 GLU 3.6 0.2 - - - -
576 ASN* 2.7 23.9 + - - -
616 LEU* 1.3 71.0 - - - +
636 THR* 1.3 64.6 + - - +
796 LEU* 3.7 35.0 - - + -
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Residues in contact with THR 63 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236 THR* 4.0 18.8 - - + -
246 VAL 3.3 11.2 - - - +
256 ALA* 4.0 7.3 - - + +
546 HIS 3.7 0.7 - - - +
556 ILE* 3.4 6.8 - - - -
566 GLU* 2.8 52.1 + - - +
616 LEU* 3.3 21.3 - - - +
626 THR* 1.3 79.6 + - - +
646 LEU* 1.3 60.7 + - - +
656 ILE* 3.7 23.7 + - + +
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Residues in contact with LEU 64 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226 LEU 3.4 1.3 - - - +
236 THR* 3.3 6.8 - - - -
246 VAL* 2.9 41.7 + - + +
386 TRP* 3.9 47.6 - - + +
456 ILE* 4.4 15.5 - - + -
536 PHE* 4.8 1.6 - - + -
546 HIS 3.8 2.2 - - - +
556 ILE* 3.9 24.9 - - + -
626 THR 4.3 0.4 - - - -
636 THR* 1.3 72.4 - - - +
656 ILE* 1.3 66.5 + - - +
666 ILE* 4.1 22.7 - - + -
776 TYR* 4.0 19.5 - - + -
946 ILE* 4.1 10.1 - - + -
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Residues in contact with ILE 65 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216 VAL* 4.0 11.4 - - + -
226 LEU 3.3 7.4 - - - +
236 THR* 3.5 20.6 - - + +
526 ARG 3.6 0.7 - - - +
536 PHE* 3.4 5.9 - - - +
546 HIS* 2.7 62.0 + - + +
566 GLU* 4.4 18.6 - - + +
636 THR* 3.7 27.8 - - + +
646 LEU* 1.3 73.4 - - - +
666 ILE* 1.3 65.7 + - - +
676 MET* 4.0 23.8 - - + -
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Residues in contact with ILE 66 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216 VAL* 4.3 0.7 - - - -
226 LEU* 2.8 48.3 + - + +
526 ARG* 3.7 26.5 - - - +
536 PHE* 3.6 36.6 - - + -
646 LEU* 4.1 13.2 - - + -
656 ILE* 1.3 75.8 - - - +
676 MET* 1.3 61.2 + - - +
696 VAL* 3.4 18.2 - - + +
736 ASP* 3.7 15.0 - - + +
776 TYR* 3.8 19.7 - - + +
946 ILE* 4.0 19.7 - - + -
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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