Contacts of the strand formed by residues 484 - 489 (chain A) in PDB entry 1UPB
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 484 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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457A THR 3.1 7.1 + - - -
458A PHE* 3.2 27.3 - - + +
459A LEU 2.8 25.9 + - - +
482A PRO 4.3 5.8 - - - +
483A ILE* 1.3 73.9 - - - +
485A THR* 1.3 62.2 + - - +
486A VAL* 4.1 1.1 + - + +
543A LEU* 4.1 17.9 - - + -
546A GLY* 3.5 36.1 - - - +
547A ALA* 3.9 5.4 - - - +
551A ARG 5.7 0.2 - - - +
553A PHE* 3.5 14.1 - - + +
555A ILE* 4.1 25.6 - - + -
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Residues in contact with THR 485 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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442A ILE* 5.5 0.2 - - - +
459A LEU* 3.3 24.4 - - + +
461A ALA* 5.3 0.2 - - + -
466A PHE* 3.8 29.0 - - + -
473A LEU* 5.3 3.3 - - - +
476A ILE* 5.0 6.9 - - - +
483A ILE* 3.7 15.4 + - - +
484A VAL* 1.3 75.0 - - - +
486A VAL* 1.3 60.7 + - - +
487A VAL* 4.0 8.3 - - + -
553A PHE 2.9 13.3 + - - -
554A LEU* 3.3 18.1 - - + +
555A ILE* 2.8 35.3 + - - +
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Residues in contact with VAL 486 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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387A VAL* 3.7 26.9 - - + -
391A MET* 4.0 23.1 - - + -
459A LEU 2.8 11.8 + - - +
460A ILE* 3.3 4.4 - - + +
461A ALA 3.0 25.3 + - - +
484A VAL* 5.0 1.6 - - + +
485A THR* 1.3 77.3 - - - +
487A VAL* 1.3 62.5 + - - +
488A VAL* 4.2 7.9 - - + -
539A LEU* 4.7 4.3 - - + -
543A LEU* 3.9 28.3 - - + -
555A ILE* 3.3 12.3 - - + +
557A VAL* 3.9 20.9 - - + -
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Residues in contact with VAL 487 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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461A ALA* 3.2 8.7 - - + +
462A GLY 4.2 1.1 - - - -
463A ASP* 4.1 20.0 - - - +
466A PHE* 3.8 30.7 - - + -
485A THR* 4.0 5.6 - - + -
486A VAL* 1.3 73.0 - - - +
488A VAL* 1.3 64.4 + - - +
489A ASN* 3.6 2.0 + - + -
519A PHE* 4.0 28.7 - - + -
554A LEU* 3.9 26.7 - - + -
555A ILE 2.9 11.0 + - - +
556A GLU* 3.6 5.7 - - + +
557A VAL 3.0 24.8 + - - +
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Residues in contact with VAL 488 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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384A VAL* 4.5 4.9 - - + -
387A VAL* 4.0 29.6 - - + -
413A PHE* 3.9 29.6 - - + -
460A ILE* 4.0 12.6 - - + -
461A ALA 2.8 20.4 + - - +
462A GLY* 3.3 6.2 - - - -
463A ASP* 3.2 20.0 + - - +
486A VAL* 3.8 5.4 + - + -
487A VAL* 1.3 69.8 - - - +
489A ASN* 1.3 59.2 + - - +
490A ASN* 4.1 1.0 + - - +
557A VAL* 3.5 5.6 - - + -
559A VAL* 3.8 28.2 - - + +
561A TYR* 4.3 7.9 + - - +
600A TPP 5.6 0.5 + - - -
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Residues in contact with ASN 489 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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463A ASP* 3.2 21.6 - - + +
487A VAL* 4.4 1.3 - - + +
488A VAL* 1.3 72.1 - - - +
490A ASN* 1.3 58.9 + - - +
491A ASP* 2.8 40.8 + - - +
517A VAL 3.6 8.9 + - - +
519A PHE* 3.6 17.8 - - + -
556A GLU* 2.8 33.9 + - + +
557A VAL 3.0 13.8 + - - +
558A PRO* 3.6 6.7 - - + +
559A VAL* 3.1 22.5 + - - +
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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