Contacts of the strand formed by residues 646 - 653 (chain C) in PDB entry 1UEX
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 VAL 646 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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601C THR* 5.0 0.2 - - + -
606C PHE* 3.7 46.0 - - + -
609C ILE* 5.1 0.4 - - + -
616C ARG* 3.5 15.3 - - + +
618C ALA* 4.4 11.9 - - + -
641C LEU* 2.8 38.2 + - + +
642C LYS* 4.4 2.5 + - - -
644C LYS* 3.7 26.0 - - + +
645C LYS* 1.3 76.1 - - - +
647C ILE* 1.3 70.6 + - - +
648C VAL* 3.4 11.2 - - + +
672C ASN* 4.9 0.2 - - - +
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Residues in contact with ILE 647 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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615C SER* 5.0 6.1 - - - -
616C ARG 2.6 18.5 + - - +
617C ILE* 3.2 9.0 - - + -
618C ALA 2.7 30.9 + - - -
645C LYS 4.3 6.7 - - - +
646C VAL* 1.3 77.4 - - - +
648C VAL* 1.3 56.9 + - - +
649C ILE* 3.6 13.5 - - + -
671C GLU* 3.6 37.0 - - + +
672C ASN* 3.4 14.6 - - - +
697C LEU* 4.0 41.5 - - + +
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Residues in contact with VAL 648 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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598C LEU* 4.6 10.5 - - + -
618C ALA* 3.5 18.2 - - + +
620C LEU* 4.5 11.7 - - + -
638C VAL* 5.4 6.3 - - + +
641C LEU* 3.4 29.4 - - + -
646C VAL* 3.4 16.4 - - + +
647C ILE* 1.3 73.2 - - - +
649C ILE* 1.3 62.5 + - - +
650C PRO* 3.0 5.5 - - - +
665C ILE* 3.4 32.7 - - + +
672C ASN* 2.9 38.0 + - - +
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Residues in contact with ILE 649 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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617C ILE* 3.7 23.8 - - + -
618C ALA 2.8 12.0 + - - +
619C LEU* 3.7 20.3 - - + -
620C LEU* 3.1 20.0 + - - -
647C ILE* 3.6 11.9 - - + -
648C VAL* 1.3 71.4 - - - +
650C PRO* 1.3 61.1 - - - +
651C VAL* 3.3 6.3 + - + +
671C GLU 3.1 28.3 - - - +
673C LYS 3.2 23.1 - - - +
675C PHE* 3.7 23.6 - - + -
693C TYR* 3.8 10.3 - - + -
694C LEU* 3.9 12.6 - - + -
697C LEU* 4.5 0.9 - - + -
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Residues in contact with PRO 650 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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620C LEU* 4.0 11.2 - - + +
622C MET* 4.9 3.1 - - - -
648C VAL 3.0 13.6 - - - +
649C ILE* 1.3 81.2 - - - +
651C VAL* 1.3 62.2 + - - +
652C GLY 4.0 0.8 + - - -
662C ILE* 4.1 25.3 - - + +
665C ILE* 3.6 35.2 - - + -
672C ASN 3.9 5.2 - - - +
673C LYS 3.7 8.4 - - - +
674C ALA* 3.4 22.7 - - + +
675C PHE 3.1 21.5 + - - +
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Residues in contact with VAL 651 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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536C PHE* 6.0 0.4 - - + -
619C LEU* 4.0 20.4 - - + -
620C LEU 3.1 10.6 + - - +
621C LEU* 3.7 27.3 - - + -
622C MET* 2.9 33.2 + - - +
649C ILE* 3.7 15.3 - - + +
650C PRO* 1.3 76.8 - - - +
652C GLY* 1.3 59.8 + - - +
653C ILE* 3.8 14.6 + - + +
675C PHE* 3.4 20.0 - - + +
677C LEU* 4.1 17.9 - - + -
683C LEU* 4.6 2.5 - - + -
690C ILE* 5.0 8.1 - - + -
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Residues in contact with GLY 652 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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622C MET 3.5 4.5 - - - -
650C PRO 4.0 1.2 - - - -
651C VAL* 1.3 73.5 - - - +
653C ILE* 1.3 61.7 + - - +
654C GLY 5.1 0.2 - - - -
657C ALA* 3.9 6.3 - - - -
662C ILE* 3.7 24.6 - - - +
675C PHE 2.6 14.4 + - - +
676C VAL* 4.4 5.4 - - - -
677C LEU* 2.7 34.4 + - - +
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Residues in contact with ILE 653 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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525C LEU* 4.9 1.3 - - + -
533C LEU* 3.6 30.7 - - + -
621C LEU* 4.3 15.3 - - + -
622C MET 2.9 11.9 + - - +
623C ALA* 3.3 31.9 - - + +
651C VAL* 4.0 13.9 - - + +
652C GLY* 1.3 79.7 - - - +
654C GLY* 1.3 71.6 + - - +
657C ALA* 3.9 5.9 + - - +
677C LEU* 3.7 8.1 - - + -
679C SER 3.5 5.4 - - - +
680C VAL* 3.4 39.9 - - + +
683C LEU* 4.1 16.6 - - + -
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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