Contacts of the strand formed by residues 557 - 565 (chain A) in PDB entry 1TF4
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 ARG 557 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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482A MET* 4.0 32.4 - - + +
483A ILE 3.1 13.7 - - - +
484A ARG* 4.0 22.3 - - - +
522A GLN* 4.0 5.2 - - - +
548A ILE* 4.0 2.2 - - - -
553A GLN* 3.2 47.3 + - - +
554A SER* 3.1 16.0 + - - +
555A GLU 3.3 2.2 + - - -
556A HIS* 1.3 89.6 - - + +
558A ARG* 1.3 83.6 + - - +
559A GLU* 5.3 2.4 + - - +
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Residues in contact with ARG 558 (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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482A MET* 3.5 4.4 - - - -
483A ILE* 2.9 37.0 + - + +
522A GLN* 3.4 26.1 - - + +
523A CYS* 4.2 22.4 - - - -
546A GLU* 2.9 32.8 + - + +
547A LYS* 3.3 31.6 + - - +
548A ILE* 3.6 27.1 - - + +
554A SER 3.2 15.0 + - - -
555A GLU* 3.4 16.8 + - - +
557A ARG* 1.3 91.1 + - - +
559A GLU* 1.3 61.1 + - - +
560A VAL* 3.8 1.7 + - + +
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Residues in contact with GLU 559 (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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480A LYS* 3.4 27.6 + - + +
481A ALA 3.6 9.2 - - - +
482A MET* 3.7 23.9 - - + +
520A TYR* 3.6 29.2 - - + +
521A ASN* 3.9 1.7 - - - -
522A GLN* 2.8 41.1 + - - +
557A ARG* 4.4 2.9 + - - +
558A ARG* 1.3 72.3 - - - +
560A VAL* 1.3 68.7 + - - +
561A GLN* 3.0 26.0 - - + +
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Residues in contact with VAL 560 (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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479A ILE 3.9 0.9 - - - +
481A ALA* 2.7 43.7 + - + +
483A ILE* 4.9 2.5 - - + -
499A PHE* 4.1 23.6 - - + -
520A TYR 4.4 0.4 - - - -
521A ASN* 3.4 28.3 - - - +
523A CYS* 3.9 23.1 - - + -
541A ILE* 3.9 16.6 - - + -
543A CYS* 4.5 0.7 - - - -
558A ARG 4.3 6.7 - - - +
559A GLU* 1.3 79.6 - - - +
561A GLN* 1.3 61.4 + - - +
562A PHE* 3.9 20.6 + - + -
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Residues in contact with GLN 561 (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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470A ASN* 3.5 27.0 + - - +
478A GLU* 5.0 3.4 + - + -
479A ILE 3.4 6.5 - - - +
480A LYS* 4.1 16.8 + - + +
518A SER* 2.6 30.8 + - - +
519A ALA* 4.8 10.6 - - - +
520A TYR* 3.1 40.5 + - - +
521A ASN* 4.2 3.5 - - - +
559A GLU* 3.0 27.6 - - + +
560A VAL* 1.3 75.6 - - - +
562A PHE* 1.3 61.3 + - - +
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Residues in contact with PHE 562 (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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477A THR 3.8 1.0 - - - +
478A GLU* 3.4 4.1 - - - +
479A ILE* 2.9 64.0 + - + -
481A ALA* 4.2 4.9 - - + -
499A PHE* 4.0 24.9 - + - -
501A TYR* 3.9 30.3 - + + -
516A VAL* 4.4 15.9 - - + -
517A SER 3.4 7.9 - - - +
518A SER* 4.8 1.8 - - - +
521A ASN* 5.6 0.9 - - - +
525A THR* 6.1 1.3 - - + -
526A PRO* 6.1 0.2 - - + -
539A VAL* 4.8 7.9 - - + -
541A ILE* 4.5 12.6 - - + -
560A VAL* 3.9 20.0 - - + -
561A GLN* 1.3 75.9 - - - +
563A ARG* 1.3 59.4 + - - +
564A ILE* 3.9 32.3 - - + -
591A ILE* 5.2 1.1 - - + -
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Residues in contact with ARG 563 (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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471A THR* 4.6 7.7 + - - +
476A PHE* 3.5 61.2 - - + -
477A THR 3.3 3.6 - - - -
478A GLU* 2.8 38.0 + - + +
515A THR 3.3 2.1 - - - +
516A VAL* 3.2 6.3 - - - -
517A SER* 2.8 48.2 + - - +
518A SER* 5.1 0.4 - - - +
562A PHE* 1.3 73.9 - - - +
564A ILE* 1.3 64.0 + - - +
565A ALA* 4.4 8.1 - - + +
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Residues in contact with ILE 564 (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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476A PHE* 3.2 4.2 - - - -
477A THR* 2.8 36.8 + - + +
479A ILE* 5.9 0.4 - - + -
501A TYR* 3.7 37.7 - - + -
503A PHE* 4.6 6.3 - - + -
514A ILE* 3.8 21.1 - - + -
515A THR 3.6 3.4 - - - +
516A VAL* 4.6 4.9 - - + +
539A VAL* 3.9 23.6 - - + -
562A PHE* 3.9 24.5 - - + -
563A ARG* 1.3 74.1 - - - +
565A ALA* 1.3 58.1 + - - +
566A GLY 3.9 0.5 + - - -
570A TRP* 3.6 31.8 - - + -
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Residues in contact with ALA 565 (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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475A THR 4.3 1.3 - - - +
476A PHE* 3.7 17.3 - - + -
513A ASP 3.8 2.9 - - - +
514A ILE* 3.3 8.7 - - - +
515A THR* 2.9 45.6 + - - +
563A ARG* 3.8 11.4 + - + -
564A ILE* 1.3 72.3 - - - +
566A GLY* 1.3 57.9 + - - +
567A GLY 3.7 2.0 - - - +
570A TRP* 4.9 0.2 - - - -
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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