Contacts of the strand formed by residues 487 - 492 (chain A) in PDB entry 3BMW
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 487 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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344A GLN* 3.6 34.3 - - + +
347A ALA* 3.9 17.0 - - + -
432A VAL* 4.5 6.1 - - + -
433A ALA 3.2 9.4 - - - +
434A ILE* 4.0 17.3 - - + -
458A ASP* 4.2 0.7 - - - +
460A LEU* 3.9 24.5 - - + +
464A LEU* 3.0 35.9 + - + +
466A GLY* 3.5 11.1 + - - -
485A GLY 4.3 1.1 - - - +
486A GLU* 1.3 80.8 - - - +
488A ALA* 1.3 67.9 + - - +
489A VAL* 4.6 1.6 - - + -
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Residues in contact with ALA 488 (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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431A LEU 3.9 0.5 - - - +
432A VAL* 3.4 4.2 - - - +
433A ALA* 3.0 33.2 + - + +
458A ASP* 3.5 9.2 - - - +
460A LEU* 4.8 0.2 - - - -
466A GLY* 3.9 16.8 - - - -
467A ASN 4.2 1.6 - - - +
486A GLU* 4.0 7.8 - - + +
487A VAL* 1.3 75.8 - - - +
489A VAL* 1.3 66.2 + - - +
490A TRP* 3.4 34.6 - - + -
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Residues in contact with VAL 489 (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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351A THR* 4.3 9.0 - - + -
394A LEU* 4.0 19.1 - - + -
397A LEU* 4.3 15.5 - - + -
404A ILE* 5.3 0.2 - - + -
430A ALA* 5.2 6.5 - - + -
431A LEU 3.5 6.1 - - - +
432A VAL* 4.1 24.7 - - + -
457A THR 3.6 0.2 - - - +
458A ASP* 3.0 13.0 + - - +
459A VAL* 2.8 53.9 + - + +
460A LEU* 4.3 11.4 - - + -
487A VAL* 4.6 3.4 - - + -
488A ALA* 1.3 79.2 - - - +
490A TRP* 1.3 68.2 + - - +
491A GLN* 5.4 1.1 - - + -
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Residues in contact with TRP 490 (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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420A ILE* 4.9 2.0 - - + -
430A ALA* 3.4 3.6 - - - +
431A LEU* 2.8 66.8 + - + +
433A ALA* 3.7 37.0 - - + -
447A LEU* 5.3 0.9 - - + -
451A LEU* 4.1 12.9 - - + +
456A TYR* 3.6 25.8 - - + -
457A THR 3.6 21.8 - - - -
458A ASP 4.2 1.2 - - - +
459A VAL* 4.6 0.2 - - - -
467A ASN 2.9 23.7 + - - -
469A ILE* 3.4 45.8 - - + +
480A PHE* 4.0 17.0 - + - -
482A LEU* 5.4 0.2 - - + -
486A GLU* 5.2 1.6 - - - -
488A ALA* 3.4 24.9 - - + +
489A VAL* 1.3 76.8 - - - +
491A GLN* 1.3 62.0 + - - +
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Residues in contact with GLN 491 (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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397A LEU* 3.7 27.6 - - - +
400A SER* 5.0 1.3 + - - -
401A ASN* 3.0 37.3 + - - +
404A ILE* 5.8 0.2 - - + -
429A VAL 3.4 5.8 - - - +
430A ALA* 4.4 3.8 - - + -
451A LEU* 3.7 6.8 - - - +
456A TYR* 3.3 21.6 - - - +
457A THR 5.2 0.4 + - - -
459A VAL* 3.7 24.8 - - + +
489A VAL* 5.4 1.6 - - + -
490A TRP* 1.3 77.4 - - - +
492A TYR* 1.3 61.1 - - - +
493A VAL* 4.2 8.4 - - + +
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Residues in contact with TYR 492 (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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401A ASN* 4.2 0.2 + - - -
427A ASN* 3.4 21.3 - - + -
428A ASN* 3.4 4.2 - - - +
429A VAL* 2.9 35.7 + - + +
451A LEU* 3.7 16.1 - - + +
452A PRO* 3.6 35.2 - - + -
456A TYR* 4.1 10.8 - + + -
491A GLN* 1.3 76.4 - - - +
493A VAL* 1.3 72.3 + - - +
494A SER* 3.7 18.4 - - - -
703A SO4 2.6 32.9 + - - -
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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