Contacts of the strand formed by residues 639 - 647 (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 LEU 639 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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612X VAL* 4.6 4.7 - - + -
616X HIS* 3.8 20.9 - - + +
631X ILE* 5.6 0.7 - - + -
635X ILE* 3.6 20.9 - - + +
636X ARG* 3.2 17.4 + - - +
637X LYS 3.5 1.9 - - - +
638X ILE* 1.3 94.3 - - + +
640X SER* 1.3 61.6 + - - +
641X GLY 3.4 7.4 - - - +
642X TYR* 3.4 32.5 - - + +
700X ALA* 4.0 13.0 - - + -
701X VAL 3.4 16.2 - - - +
702X THR* 3.8 13.5 - - + -
703X LYS* 5.4 1.8 - - - -
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Residues in contact with SER 640 (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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336X HIS* 4.4 11.8 + - - -
337X SER* 5.5 0.3 + - - -
638X ILE 4.1 1.4 + - - -
639X LEU* 1.3 73.0 - - - +
641X GLY* 1.3 58.8 + - - +
663X LEU* 4.5 6.2 - - - +
664X ASN* 4.7 10.4 + - - +
701X VAL* 2.8 17.8 + - - +
702X THR 4.0 0.5 + - - -
703X LYS* 4.2 6.2 - - - +
706X THR* 2.5 38.3 + - - +
804X PG4 3.8 23.8 - - - -
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Residues in contact with GLY 641 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
639X LEU* 3.4 3.4 - - - +
640X SER* 1.3 83.9 + - - +
642X TYR* 1.3 71.7 + - - -
663X LEU* 3.2 22.2 - - - -
664X ASN* 4.9 0.9 - - - -
666X SER* 6.1 0.9 - - - -
700X ALA* 3.7 1.2 - - - +
701X VAL* 2.8 34.4 + - - +
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Residues in contact with TYR 642 (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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616X HIS* 2.9 33.7 + - - -
631X ILE* 3.8 11.4 - - - +
636X ARG* 5.7 1.9 + - - +
639X LEU* 3.4 22.4 - - + +
641X GLY* 1.3 80.7 - - - -
643X ILE* 1.3 58.2 + - - +
657X ASN* 2.8 26.7 + - - -
663X LEU* 3.0 16.2 + - - +
665X ILE* 3.7 19.0 - - + +
666X SER* 3.5 34.3 + - - -
674X THR* 5.0 1.0 - - - +
676X ILE* 3.7 23.3 - - + -
698X VAL* 4.1 16.2 - - + -
699X TYR 2.9 20.9 - - - +
700X ALA* 3.8 13.7 - - + -
701X VAL 4.7 0.4 - - - +
726X ILE* 3.9 5.2 - - + -
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Residues in contact with ILE 643 (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* 1.3 75.7 - - - +
644X VAL* 1.3 67.7 + - - +
645X GLU* 4.9 0.9 - - + +
655X VAL* 3.4 33.2 - - + -
657X ASN* 3.7 2.9 - - - -
663X LEU* 3.6 24.7 - - + -
698X VAL* 3.3 5.0 - - - +
699X TYR* 2.8 54.3 + - + -
701X VAL* 3.9 21.5 - - + -
718X THR* 4.0 22.0 - - + +
721X ILE* 4.3 7.9 - - + -
723X LYS* 4.0 21.5 - - + +
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Residues in contact with VAL 644 (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* 1.3 75.7 - - - +
645X GLU* 1.3 64.6 + - - +
655X VAL* 3.2 8.0 - - - +
656X ILE* 2.9 45.1 + - + -
657X ASN* 2.9 13.7 + - - +
665X ILE* 3.7 26.9 - - + -
678X PHE* 3.7 29.8 - - + -
687X LEU* 4.0 19.5 - - + -
696X VAL* 4.1 15.3 - - + -
697X ASN 3.6 3.8 - - - +
698X VAL* 4.4 5.4 - - + +
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Residues in contact with GLU 645 (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* 4.9 0.7 - - + -
644X VAL* 1.3 76.4 - - - +
646X ILE* 1.3 76.1 + - - +
653X LYS* 3.2 37.2 - - + +
654X GLU 3.4 12.6 - - - +
655X VAL* 4.5 13.9 - - + +
656X ILE* 4.5 0.7 - - - +
696X VAL* 3.4 6.9 - - - +
697X ASN* 2.8 54.6 + - - +
699X TYR* 2.4 36.4 + - + -
723X LYS* 3.5 16.5 + - - -
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Residues in contact with ILE 646 (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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645X GLU* 1.3 79.7 - - - +
647X GLU* 1.3 65.3 + - - +
652X LEU 3.9 0.5 - - - +
653X LYS* 3.4 3.5 - - - -
654X GLU* 2.8 40.6 + - + +
656X ILE* 3.6 23.8 - - + +
687X LEU* 4.6 12.1 - - + -
688X TYR 4.9 8.1 - - - +
689X ILE* 4.7 13.7 - - + -
694X TYR* 4.0 28.7 - - + -
695X LYS 3.4 9.9 - - - +
696X VAL* 4.6 10.8 - - + -
113Y SER* 5.0 14.8 - - - +
115Y VAL* 4.4 13.5 - - + -
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Residues in contact with GLU 647 (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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646X ILE* 1.3 80.6 - - - +
648X ASP* 1.3 74.9 + - - +
651X GLY* 4.0 18.3 + - - +
652X LEU 3.3 9.6 - - - +
653X LYS* 3.9 18.2 - - + -
694X TYR* 3.3 9.4 - - - +
695X LYS* 3.0 57.9 + - + +
697X ASN* 3.0 29.7 + - - +
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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