Contacts of the strand formed by residues 695 - 702 (chain X) in PDB entry 1T6B
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 LYS 695 (chain X).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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646X ILE* 3.4 8.5 - - - +
647X GLU* 3.0 65.2 + - + +
648X ASP 5.7 0.7 - - - +
693X ASN 3.8 1.1 + - - +
694X TYR* 1.3 76.2 - - - +
696X VAL* 1.3 63.8 + - - +
697X ASN* 3.9 12.3 - - - +
728X SER* 3.5 23.1 + - - +
729X LYS* 3.3 11.6 - - - +
730X LYS* 4.2 29.9 - - + +
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Residues in contact with VAL 696 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
644X VAL* 4.1 18.4 - - + -
645X GLU 3.4 4.5 - - - +
646X ILE* 4.6 3.4 - - + -
678X PHE* 3.9 30.3 - - + -
687X LEU* 4.2 8.1 - - + -
689X ILE* 4.0 28.7 - - + -
694X TYR 4.3 1.3 + - - +
695X LYS* 1.3 77.0 - - - +
697X ASN* 1.3 60.2 - - - +
698X VAL* 4.3 4.7 - - + -
727X PHE* 3.8 8.4 - - + -
728X SER* 3.5 2.9 - - - -
729X LYS 2.9 27.2 + - - -
731X GLY 5.7 0.9 - - - +
734X ILE* 3.8 26.0 - - + -
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Residues in contact with ASN 697 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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643X ILE 3.8 0.3 - - - +
644X VAL* 3.6 2.8 - - - +
645X GLU* 2.8 56.8 + - - +
647X GLU* 3.0 34.5 + - - +
653X LYS* 4.5 0.4 - - - +
695X LYS* 3.9 6.4 - - - +
696X VAL* 1.3 74.3 - - - +
698X VAL* 1.3 61.6 + - - +
699X TYR* 3.6 22.5 + - + +
725X LEU* 3.8 11.3 - - + +
727X PHE 3.3 3.8 - - - -
728X SER* 2.3 32.1 + - - -
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Residues in contact with VAL 698 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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627X LEU* 4.0 13.5 - - + -
642X TYR* 4.1 16.4 - - + -
643X ILE 3.3 6.3 - - - +
644X VAL* 4.4 6.3 - - + -
676X ILE* 4.3 11.0 - - + -
678X PHE* 3.6 33.7 - - + -
696X VAL* 4.3 4.7 - - + -
697X ASN* 1.3 80.5 - - - +
699X TYR* 1.3 64.5 + - - +
725X LEU* 3.8 2.6 - - - +
726X ILE* 2.8 44.4 + - + +
727X PHE* 2.9 26.5 + - + +
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Residues in contact with TYR 699 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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642X TYR* 2.9 13.6 - - - +
643X ILE* 2.8 54.5 + - + +
645X GLU* 2.4 47.7 + - + -
653X LYS* 3.9 9.0 + - - -
697X ASN* 3.6 23.8 + - + +
698X VAL* 1.3 76.0 - - - +
700X ALA* 1.3 61.2 + - - +
701X VAL* 4.7 0.3 - - - +
723X LYS* 3.4 52.9 + - + -
724X ILE 3.2 5.4 - - - +
725X LEU* 3.8 35.1 - - + +
726X ILE* 4.2 0.4 - - - -
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Residues in contact with ALA 700 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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612X VAL* 4.1 18.2 - - + -
616X HIS* 4.6 0.2 - - - +
639X LEU* 4.0 20.6 - - + -
641X GLY 3.7 4.3 - - - +
642X TYR* 3.8 20.0 - - + -
699X TYR* 1.3 74.8 - - - +
701X VAL* 1.3 61.6 + - - +
702X THR 4.2 0.2 - - - -
723X LYS* 3.6 5.0 - - - -
724X ILE* 2.9 38.3 + - + +
726X ILE* 3.9 7.0 - - + +
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Residues in contact with VAL 701 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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639X LEU* 3.4 7.3 - - - +
640X SER* 2.8 35.7 + - - +
641X GLY 2.8 20.7 + - - +
643X ILE* 3.9 30.7 - - + -
663X LEU* 4.2 13.9 - - + -
699X TYR 4.7 0.9 - - - +
700X ALA* 1.3 79.2 - - - +
702X THR* 1.3 70.6 + - - +
705X ASN 4.1 9.4 - - - +
706X THR* 4.2 3.6 - - - +
721X ILE* 4.0 20.4 - - + -
722X LYS 4.0 9.0 - - - +
723X LYS* 4.4 6.3 - - + -
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Residues in contact with THR 702 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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605X VAL 3.9 8.5 - - - -
606X GLY* 4.0 8.3 - - - -
607X ALA 4.4 6.1 - - - +
612X VAL* 4.6 1.8 - - + -
638X ILE* 3.3 19.1 - - + +
639X LEU* 3.8 14.8 - - + -
701X VAL* 1.3 76.9 - - - +
703X LYS* 1.3 57.1 + - - +
704X GLU* 3.9 8.7 + - - -
705X ASN* 2.8 52.9 + - - +
706X THR* 3.1 14.2 + - - -
722X LYS 5.1 0.2 + - - -
724X ILE* 3.8 26.8 - - + +
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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