Contacts of the strand formed by residues 651 - 657 (chain B) in PDB entry 1UKJ
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 THR 651 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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606B GLU* 3.3 24.3 + - - -
608B LEU* 3.1 23.3 - - - +
647B MET* 3.9 20.3 - - + -
648B THR* 2.7 51.6 + - - +
649B PRO 4.7 2.6 - - - +
650B ALA* 1.3 71.6 - - - +
652B ARG* 1.3 59.8 + - - +
653B VAL 4.3 7.4 + - - -
654B ILE* 4.8 0.5 - - - +
679B HIS* 5.6 0.8 - - + +
680B GLY 4.9 2.8 - - - +
681B ALA* 3.8 17.8 + - - +
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Residues in contact with ARG 652 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
599B THR 4.9 0.4 + - - -
600B LEU* 2.7 42.1 + - - +
601B LEU* 3.7 12.6 - - + -
602B ARG* 6.4 0.2 - - - +
605B ASP* 3.8 26.0 + - + +
606B GLU 2.7 14.1 + - - +
650B ALA 3.0 3.2 + - - +
651B THR* 1.3 74.3 - - - +
653B VAL* 1.3 65.1 + - - +
680B GLY 4.8 1.6 - - - +
681B ALA* 3.6 4.6 - - - +
682B THR* 3.0 34.1 + - - -
730B LEU* 6.0 0.4 - - - +
733B ARG* 3.3 31.5 - - - +
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Residues in contact with VAL 653 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
597B LEU* 4.2 20.0 - - + -
600B LEU* 4.3 17.3 - - + -
601B LEU* 3.5 24.7 - - + -
606B GLU 3.6 2.2 + - - -
607B VAL* 3.2 22.2 - - + +
608B LEU 3.0 22.9 + - - -
651B THR* 3.8 2.6 + - - -
652B ARG* 1.3 93.2 - - + +
654B ILE* 1.3 71.0 + - - +
655B TYR* 4.4 1.8 - - + -
681B ALA* 4.7 0.7 - - - -
682B THR* 3.1 17.7 - - - +
684B VAL* 4.3 7.4 - - + -
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Residues in contact with ILE 654 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
608B LEU* 3.4 21.3 - - + -
637B MET* 3.3 32.8 - - + -
643B LEU* 4.8 5.6 - - + -
647B MET* 4.4 12.6 - - - -
651B THR* 4.8 0.2 - - - +
653B VAL* 1.3 76.0 - - - +
655B TYR* 1.3 59.8 + - - +
656B PHE* 3.6 20.9 - - + -
672B VAL* 4.3 10.1 - - + +
676B ALA* 3.5 35.9 - - + +
681B ALA* 4.0 14.1 - - + -
682B THR 2.9 6.4 + - - +
683B VAL* 3.5 8.1 - - + +
684B VAL* 2.9 27.4 + - - +
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Residues in contact with TYR 655 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
593B ILE* 3.0 37.8 - - + +
596B THR* 6.4 0.2 - - + -
597B LEU* 4.2 25.4 - - + -
607B VAL* 4.5 0.4 - - + -
608B LEU 2.9 7.1 + - - +
609B LEU* 3.3 23.1 - - + -
610B GLY 3.2 20.8 + - - -
613B LEU* 4.1 16.8 - - + -
617B THR* 3.5 25.6 - - + +
621B LEU* 5.2 1.6 - - + -
637B MET* 4.7 0.2 - - - +
653B VAL* 4.0 11.4 - - + -
654B ILE* 1.3 76.2 - - - +
656B PHE* 1.3 75.0 + - - +
657B GLU* 4.6 5.5 + - + -
684B VAL* 3.2 34.5 - - + -
686B ASP* 3.7 16.9 + - + +
706B VAL* 4.3 6.7 - - + -
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Residues in contact with PHE 656 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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610B GLY* 4.1 11.2 - - - +
613B LEU* 4.6 2.5 - - - -
637B MET* 3.7 21.1 - - + -
654B ILE* 3.6 28.0 - - + -
655B TYR* 1.3 89.8 - - - +
657B GLU* 1.3 71.5 + - - +
658B SER* 4.6 1.3 - - - -
667B ALA* 3.8 29.6 - - + -
669B ILE* 4.4 15.9 - - + -
672B VAL* 3.7 23.6 - - + -
683B VAL* 3.6 15.7 - - + -
684B VAL 3.5 2.0 + - - -
685B VAL* 3.4 34.7 - - + +
686B ASP* 2.9 23.6 + - - +
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Residues in contact with GLU 657 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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612B THR 4.4 4.8 + - - +
613B LEU* 3.5 17.9 - - + +
614B TYR* 2.8 41.6 + - - +
617B THR* 4.2 3.8 + - - -
655B TYR* 4.6 6.0 - - + -
656B PHE* 1.3 84.3 - - - +
658B SER* 1.3 63.5 + - - +
659B PRO 3.4 8.9 - - - +
660B ALA* 3.5 25.9 - - + +
661B ASN* 5.0 5.4 + - - +
665B HIS 4.4 1.7 - - - +
667B ALA* 5.2 1.4 - - - +
686B ASP* 3.6 35.9 - - + +
711B LLP 4.2 12.4 - - + +
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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