Contacts of the strand formed by residues 61 - 66 (chain 4) 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 4).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254 ALA* 4.5 11.4 - - + -
264 CYS 3.4 25.1 - - - +
274 ALA* 4.0 5.4 - - - +
284 PHE* 3.4 10.5 - - - -
564 GLU 3.8 2.6 - - - +
574 ASN* 3.5 1.7 - - - -
584 THR* 2.8 49.4 + - + +
604 ASP* 1.3 83.3 - - - +
624 THR* 1.3 62.3 + - - +
634 THR* 3.3 24.9 - - - +
155 ARG* 4.1 25.6 - - + +
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Residues in contact with THR 62 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244 VAL 3.6 1.0 - - - +
254 ALA* 3.5 0.3 - - - -
264 CYS* 2.8 45.5 + - + +
284 PHE* 3.7 13.2 - - + -
364 VAL* 3.4 8.1 - - - +
384 TRP* 2.8 28.0 + - + +
554 ILE* 4.0 0.3 - - - +
574 ASN* 2.8 23.1 + - - -
614 LEU* 1.3 72.9 - - - +
634 THR* 1.3 63.8 + - - +
644 LEU 4.3 0.4 - - - -
794 LEU* 3.7 35.2 - - + -
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Residues in contact with THR 63 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234 THR* 3.9 18.8 - - + -
244 VAL 3.3 11.0 - - - +
254 ALA* 4.1 6.8 - - + +
544 HIS 3.6 0.5 - - - +
554 ILE* 3.4 6.8 - - - -
564 GLU* 2.8 51.7 + - - +
614 LEU* 3.3 21.5 - - - +
624 THR* 1.3 80.0 + - - +
644 LEU* 1.3 62.3 + - - +
654 ILE* 3.6 23.4 + - + +
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Residues in contact with LEU 64 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224 LEU 3.5 1.3 - - - +
234 THR* 3.3 6.8 - - - -
244 VAL* 2.9 41.3 + - + +
384 TRP* 3.9 48.1 - - + +
454 ILE* 4.4 14.8 - - + -
534 PHE* 4.8 2.0 - - + -
544 HIS 3.7 2.2 - - - +
554 ILE* 3.9 24.7 - - + -
624 THR 4.3 0.4 - - - -
634 THR* 1.3 72.0 - - - +
654 ILE* 1.3 66.3 + - - +
664 ILE* 4.0 23.3 - - + -
774 TYR* 4.0 19.3 - - + -
944 ILE* 4.1 10.8 - - + -
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Residues in contact with ILE 65 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214 VAL* 4.1 10.8 - - + -
224 LEU 3.3 7.4 - - - +
234 THR* 3.5 20.4 - - + +
524 ARG 3.6 0.7 - - - +
534 PHE* 3.4 6.2 - - - +
544 HIS* 2.7 60.4 + - + +
564 GLU* 4.5 18.2 - - + +
634 THR* 3.6 30.1 - - + +
644 LEU* 1.3 73.3 - - - +
664 ILE* 1.3 65.2 + - - +
674 MET* 4.0 24.5 - - + -
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Residues in contact with ILE 66 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214 VAL* 3.5 0.8 - - - -
224 LEU* 2.8 48.8 + - + +
524 ARG* 3.7 26.5 - - - +
534 PHE* 3.6 37.5 - - + -
644 LEU* 4.0 14.1 - - + -
654 ILE* 1.3 74.2 - - - +
674 MET* 1.3 62.1 + - - +
694 VAL* 3.4 18.3 - - + +
734 ASP* 3.7 15.3 - - + +
774 TYR* 3.8 13.7 - - + +
944 ILE* 4.0 25.6 - - + -
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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