Contacts of the strand formed by residues 530 - 534 (chain B) in PDB entry 4L28
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 VAL 530 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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421B ALA* 3.6 7.4 - - - +
422B PRO* 3.1 40.6 - - + +
424B THR* 6.5 0.2 - - - -
447B PRO* 4.2 18.8 - - + -
449B VAL* 4.8 3.6 - - + -
455B ILE* 4.0 27.8 - - + -
510B LEU* 4.4 13.2 - - + -
511B VAL 3.6 5.8 - - - +
512B VAL* 4.3 3.1 - - + -
528B GLN 3.5 9.4 + - - +
529B MET* 1.3 75.9 - - - +
531B PHE* 1.3 57.5 + - - +
532B GLY 3.4 26.0 - - - +
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Residues in contact with PHE 531 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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419B LEU* 3.9 10.3 - - + +
420B SER* 3.3 3.3 + - - -
421B ALA* 3.3 26.9 + - + +
492B LEU* 3.9 34.8 - - + -
511B VAL* 2.9 20.3 + - + +
512B VAL* 3.7 7.4 - - - -
513B HIS* 3.4 51.8 - + + -
529B MET* 3.6 29.8 - - + -
530B VAL* 1.3 71.9 - - - +
532B GLY* 1.3 56.3 + - - +
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Residues in contact with GLY 532 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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419B LEU* 4.6 7.2 - - - -
420B SER 3.7 13.2 - - - -
422B PRO* 4.0 4.3 - - - -
510B LEU* 3.6 1.4 - - - -
511B VAL* 3.0 36.8 + - - +
530B VAL* 3.1 12.0 - - - +
531B PHE* 1.3 81.1 - - - +
533B VAL* 1.3 64.1 + - - -
534B VAL* 4.9 0.2 - - - -
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Residues in contact with VAL 533 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
419B LEU* 4.9 3.7 - - - +
420B SER 4.8 1.6 + - - -
422B PRO* 4.3 19.7 - - + -
445B GLN* 3.4 32.1 + - - +
447B PRO* 4.6 3.6 - - + -
458B MET* 4.2 11.7 - - - -
508B PHE* 3.5 30.5 - - + -
509B ALA 3.7 3.1 - - - +
510B LEU* 3.5 23.1 - - + -
530B VAL* 4.5 0.9 - - + -
532B GLY* 1.3 74.8 - - - -
534B VAL* 1.3 69.5 + - - +
535B THR* 4.9 2.0 - - + -
538B ASP* 3.7 9.9 - - - +
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Residues in contact with VAL 534 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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414B VAL* 4.7 6.3 - - + -
417B LEU* 3.9 16.2 - - + -
419B LEU* 3.9 24.2 - - + -
490B ILE* 4.8 4.3 - - + -
499B LEU* 3.8 31.6 - - + -
503B LEU* 4.3 1.4 - - - +
507B HIS 3.7 2.3 - - - +
509B ALA* 2.9 40.7 + - - +
511B VAL* 4.6 8.3 - - + -
533B VAL* 1.3 81.9 - - - +
535B THR* 1.3 75.2 + - - +
538B ASP* 3.6 11.4 - - + -
539B LEU 4.8 1.3 - - - +
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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