Contacts of the strand formed by residues 535 - 539 (chain A) in PDB entry 4FM9
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 535 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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453A THR 5.2 5.6 - - - +
454A GLU* 6.3 0.9 - - - +
455A CYS 3.2 5.2 + - - +
456A THR* 2.9 22.7 - - + -
457A LEU 2.7 28.6 + - - -
533A TYR* 4.2 0.7 - - - +
534A GLY* 1.3 83.1 - - - +
536A ILE* 1.3 64.8 + - - +
568A ARG* 4.0 15.0 - - - +
569A PHE* 3.2 10.8 - - - +
571A GLU* 3.2 35.1 + - - +
635A ARG* 5.2 1.6 - - - +
637A GLN* 3.6 19.6 + - - +
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Residues in contact with ILE 536 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
457A LEU* 3.2 36.8 - - + +
459A LEU* 3.6 29.2 - - + -
514A VAL* 3.8 24.0 - - + -
533A TYR* 4.4 6.1 - - + -
535A LYS* 1.3 79.0 - - - +
537A MET* 1.3 54.4 + - - +
538A ILE* 3.8 0.7 + - - +
553A LEU* 4.6 12.9 - - + +
557A ILE* 6.2 0.4 - - + -
569A PHE* 2.8 44.8 + - + +
570A LEU* 3.4 9.8 - - + +
571A GLU* 2.7 32.3 + - - +
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Residues in contact with MET 537 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
456A THR* 4.5 6.9 - - - +
457A LEU 2.7 11.0 + - - +
458A ILE* 2.9 40.1 - - + +
459A LEU 2.7 30.2 + - - +
481A TYR* 4.4 13.7 - - + -
535A LYS 4.1 1.0 - - - -
536A ILE* 1.3 72.3 - - - +
538A ILE* 1.3 57.3 + - - +
539A MET* 6.4 0.2 - - - -
571A GLU* 2.8 29.6 - - + +
572A GLU 4.7 2.0 - - - +
573A PHE* 3.7 51.8 - - + +
628A PHE* 4.7 9.2 - - + -
631A MET* 5.2 3.4 - - + +
635A ARG* 4.8 15.9 - - - -
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Residues in contact with ILE 538 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
459A LEU* 3.4 11.0 - - + +
486A LEU* 4.5 7.2 - - + -
536A ILE 3.8 1.2 + - - +
537A MET* 1.3 73.0 - - - +
539A MET* 1.3 62.8 + - - +
540A THR* 3.8 10.1 + - + +
549A ILE* 3.9 15.5 - - + +
550A LYS* 3.3 50.2 - - + +
553A LEU* 3.8 30.5 - - + -
570A LEU* 6.4 1.1 - - + -
571A GLU 2.6 19.3 + - - +
572A GLU* 3.4 15.2 - - + +
573A PHE 3.0 19.3 + - - +
638A PHE* 4.6 5.6 - - + -
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Residues in contact with MET 539 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
458A ILE* 3.8 12.8 - - + -
459A LEU 2.8 9.5 + - - -
460A THR* 3.4 45.0 - - + -
461A GLU 3.4 3.1 + - - -
465A ALA 4.6 2.7 - - - +
468A LEU* 4.5 11.9 - - + -
469A ALA* 4.1 16.8 - - - -
537A MET* 3.9 0.6 + - - -
538A ILE* 1.3 74.9 - - - +
540A THR* 1.3 64.9 + - - +
573A PHE* 3.5 34.3 - - + +
575A THR* 4.1 16.6 - - + -
616A LEU* 3.6 36.2 - - + +
628A PHE* 4.8 7.4 - - + -
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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
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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