Contacts of the strand formed by residues 589 - 600 (chain U) in PDB entry 6FF7
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 589 (chain U).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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430U GLU 5.8 0.2 - - - +
433U ILE* 5.9 0.2 - - - -
434U TRP* 3.9 20.3 - - + +
482U ARG* 4.6 15.0 - - + +
486U GLU* 3.9 26.7 - - + -
566U THR 4.0 4.5 - - - -
567U VAL* 4.6 0.9 - - - +
583U PHE 5.2 1.3 - - - +
584U ILE* 3.0 28.9 + - + +
587U VAL* 3.5 2.5 - - + -
588U GLY* 1.3 74.9 - - - +
590U VAL* 1.3 59.2 + - - +
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Residues in contact with VAL 590 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
429U THR 4.6 1.2 - - - +
430U GLU* 4.3 26.2 + - + +
433U ILE* 3.0 26.8 - - - +
482U ARG* 5.5 1.1 - - - -
485U ILE* 4.6 0.2 - - - +
566U THR* 2.8 23.7 + - - +
567U VAL 5.4 0.2 - - - -
568U ARG* 5.0 8.5 - - + +
588U GLY 3.3 5.1 + - - +
589U LEU* 1.3 75.2 - - - +
591U TYR* 1.3 60.5 + - + +
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Residues in contact with TYR 591 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
433U ILE* 4.8 2.0 - - - -
481U ILE 2.6 1.1 - - - -
482U ARG* 3.9 3.6 - - - +
485U ILE* 0.7 94.8 - - + +
564U LEU 4.4 0.2 - - - -
566U THR* 3.3 12.7 + - - -
590U VAL* 1.3 78.4 - - + +
592U VAL* 1.3 53.4 - - - +
593U ARG* 6.2 1.1 - - + -
649U VAL* 5.2 17.5 - - + +
652U THR* 6.2 0.7 - - - -
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Residues in contact with VAL 592 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
433U ILE* 5.5 0.2 - - - +
480U GLU 2.7 10.8 - - - +
481U ILE* 0.9 170.8 + - - +
482U ARG* 1.9 24.4 - - - +
483U GLN 2.9 0.7 - - - +
484U ASP 2.9 4.3 - - - +
485U ILE 3.0 4.9 - - - +
591U TYR* 1.3 73.9 - - - +
593U ARG* 1.3 56.6 + - - +
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Residues in contact with ARG 593 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
480U GLU 4.9 0.9 - - - -
481U ILE* 3.9 2.7 - - - +
484U ASP* 2.7 8.0 - - - +
564U LEU* 2.6 50.1 + - + +
591U TYR* 6.2 0.9 - - + -
592U VAL* 1.3 75.0 - - - +
594U GLY* 1.3 62.8 + - - +
633U GLN* 6.6 0.2 - - + -
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Residues in contact with GLY 594 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
480U GLU* 5.4 2.9 + - - +
481U ILE* 5.2 0.6 - - - +
562U CYS 3.6 6.5 - - - -
563U PHE* 4.4 3.1 - - - -
564U LEU* 5.6 1.0 - - - +
593U ARG* 1.3 81.0 - - - +
595U CYS* 1.3 63.0 + - - +
628U PHE 4.6 1.2 - - - +
629U LEU* 4.6 9.7 - - - +
630U ASP* 4.7 6.5 + - - +
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Residues in contact with CYS 595 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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561U VAL* 3.2 8.3 - - - +
562U CYS* 2.8 39.3 + - + +
564U LEU* 5.7 6.3 - - + -
594U GLY* 1.3 77.6 - - - +
596U GLU* 1.3 61.3 + - - +
627U VAL* 4.0 16.4 - - + -
628U PHE 3.3 15.3 - - - +
629U LEU* 4.9 2.7 - - + +
630U ASP 5.6 0.4 - - - +
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Residues in contact with GLU 596 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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559U HIS* 4.9 11.4 - - - +
560U ASP 3.4 7.2 - - - +
561U VAL* 5.0 2.9 - - + -
595U CYS* 1.3 75.5 - - - +
597U ILE* 1.3 67.4 + - - +
627U VAL* 3.2 4.0 - - - -
628U PHE* 2.7 47.7 + - + +
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Residues in contact with ILE 597 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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556U LEU* 5.2 7.6 - - + -
557U ARG 3.4 25.6 - - - +
558U LYS* 3.3 1.9 - - - +
559U HIS* 2.9 28.6 + - - -
560U ASP* 2.7 19.2 + - + +
562U CYS* 5.4 1.7 - - + +
595U CYS 4.3 0.2 - - - -
596U GLU* 1.3 71.7 - - - +
598U GLN* 1.3 59.2 + - - +
599U GLY* 4.6 6.5 - - - +
625U PHE* 5.7 7.2 - - + -
626U ARG 4.0 4.5 - - - +
627U VAL* 4.5 3.6 - - - +
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Residues in contact with GLN 598 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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558U LYS* 3.5 22.6 - - - +
596U GLU 3.3 3.2 + - - +
597U ILE* 1.3 73.2 - - - +
599U GLY* 1.3 58.7 + - - +
607U VAL* 5.6 5.9 - - + +
608U ILE 4.7 2.9 - - - +
626U ARG* 2.8 25.4 + - + +
627U VAL* 4.6 5.2 - - - +
628U PHE* 5.2 1.8 - - + +
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Residues in contact with GLY 599 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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557U ARG 5.8 0.9 - - - -
558U LYS 5.4 3.6 - - - -
597U ILE* 3.6 6.1 - - - +
598U GLN* 1.3 82.4 - - - +
600U MET* 1.3 65.3 + - - -
607U VAL* 4.9 8.1 - - - +
608U ILE 4.1 13.5 - - - -
625U PHE* 3.6 4.4 - - - -
626U ARG* 2.8 30.1 + - - +
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Residues in contact with MET 600 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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554U GLU* 6.1 1.8 - - - +
556U LEU 5.8 6.0 + - - +
599U GLY* 1.3 71.7 - - - -
601U LEU* 1.3 65.4 + - - +
607U VAL* 3.7 1.3 - - - -
608U ILE* 2.8 37.4 + - + +
623U ARG* 6.2 3.4 - - + -
624U THR 3.5 10.3 - - - +
625U PHE* 4.2 5.6 - - + +
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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