Contacts of the strand formed by residues 556 - 563 (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 GLY 556 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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554A THR 3.4 1.9 + - - -
555A PRO* 1.3 73.9 - - - +
557A LYS* 1.3 61.1 + - - -
558A TYR* 3.3 14.8 - - - -
577A ASN* 3.8 10.1 - - - -
578A ILE* 2.8 29.6 + - - +
608A ALA* 4.1 9.1 - - - +
612A ASN* 5.9 0.2 - - - -
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Residues in contact with LYS 557 (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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275A ASN 4.4 8.5 + - - -
276A GLU* 2.7 40.4 + - - -
316A ASN* 4.4 12.9 - - - +
556A GLY* 1.3 71.9 - - - -
558A TYR* 1.3 69.1 + - - +
559A ASN* 5.4 0.9 - - - +
575A ASN* 3.7 36.2 + - + +
576A ILE 3.3 3.8 - - - +
577A ASN* 3.8 27.4 - - - +
617A LYS* 5.3 5.9 - - - +
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Residues in contact with TYR 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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531A PHE* 3.7 30.5 - - + -
532A GLY* 4.0 11.2 - - - +
534A THR* 5.9 0.2 - - - -
553A VAL* 3.4 22.2 - - + +
554A THR* 2.6 45.9 + - - -
556A GLY* 3.3 24.0 - - - -
557A LYS* 1.3 76.7 - - - +
559A ASN* 1.3 66.0 + - - +
560A ILE* 3.9 5.0 + - + -
574A ASN 4.1 0.3 - - - -
575A ASN 3.4 1.7 + - - -
576A ILE* 2.8 38.7 + - + +
578A ILE* 3.6 20.4 - - + -
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Residues in contact with ASN 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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530A LEU 3.6 1.0 - - - +
532A GLY* 2.9 30.7 + - - +
557A LYS 5.4 0.3 - - - -
558A TYR* 1.3 74.9 + - - +
560A ILE* 1.3 63.0 + - - +
561A SER* 3.9 1.4 + - - -
572A THR* 4.3 11.4 + - + +
573A TYR 3.6 3.4 - - - -
574A ASN* 3.3 29.8 + - - +
575A ASN* 3.2 23.4 + - - +
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Residues in contact with ILE 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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501A ILE* 3.8 10.2 - - + +
504A VAL* 4.5 10.5 - - + -
515A ILE* 4.3 5.6 - - + -
517A ILE* 3.8 31.2 - - + -
529A VAL* 4.0 7.6 - - + -
530A LEU 3.4 6.7 - - - +
531A PHE* 3.5 42.0 - - + -
558A TYR* 4.3 3.1 - - + +
559A ASN* 1.3 75.8 - - - +
561A SER* 1.3 63.6 + - - +
572A THR* 3.2 5.5 - - - -
573A TYR* 2.8 41.7 + - + +
576A ILE* 3.5 36.3 - - + -
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Residues in contact with SER 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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501A ILE* 4.0 3.4 - - - -
529A VAL* 3.5 6.1 - - - +
530A LEU* 2.8 51.6 + - - +
532A GLY 4.4 5.0 + - - -
559A ASN 3.9 1.0 + - - -
560A ILE* 1.3 76.7 - - - +
562A LEU* 1.3 62.2 + - - +
563A LYS* 5.0 0.7 + - - -
569A THR* 4.5 10.2 - - - +
570A SER* 3.7 15.3 - - - -
571A ASN 4.0 5.4 - - - -
572A THR* 4.1 15.3 - - - -
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Residues in contact with LEU 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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499A PRO* 4.1 13.0 - - + -
501A ILE* 4.1 6.7 - - + -
517A ILE* 4.4 7.4 - - + -
522A PHE* 3.6 49.1 - - + -
528A GLN 3.4 6.1 - - - +
529A VAL* 4.3 7.9 - - + +
530A LEU* 6.0 0.7 - - - -
541A TRP* 3.6 23.8 - - + -
546A VAL* 3.8 24.5 - - + -
561A SER* 1.3 75.4 - - - +
563A LYS* 1.3 70.8 + - - +
564A THR 4.1 0.9 - - - +
568A ALA 3.8 0.3 - - - +
569A THR* 3.4 3.3 - - - +
570A SER* 2.8 41.5 + - - +
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Residues in contact with LYS 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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527A GLY* 3.4 2.3 - - - -
528A GLN* 2.8 61.9 + - + +
530A LEU* 3.6 27.2 - - + +
541A TRP* 3.5 3.1 - - - -
561A SER* 5.0 0.8 + - - -
562A LEU* 1.3 79.5 - - - +
564A THR* 1.3 67.5 + - - +
567A GLY* 4.9 9.2 - - - +
568A ALA 3.2 4.9 - - - +
569A THR* 3.2 38.1 + - + +
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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