Contacts of the strand formed by residues 551 - 557 (chain B) in PDB entry 2VGB
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 LEU 551 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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449A ARG* 3.3 54.5 - - + +
451A PRO* 4.5 8.1 - - + -
454A VAL* 4.7 1.6 - - + -
466B CYS* 3.6 39.5 - - + +
468B ALA* 3.7 2.9 - - - +
469B ALA* 3.3 24.7 + - - +
549B GLY 5.0 1.3 - - - +
550B ASP* 1.3 79.3 - - - +
552B VAL* 1.3 63.8 + - - +
570B VAL* 4.3 17.0 - - + -
571B LEU 3.4 14.4 - - - +
572B SER* 3.8 19.5 - - - -
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Residues in contact with VAL 552 (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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468B ALA* 4.6 0.9 - - - -
469B ALA* 5.4 0.4 - - + -
470B ALA* 3.1 39.5 - - + +
472B ILE* 4.1 20.9 - - + -
537B ILE* 5.0 0.9 - - + -
546B LEU* 4.5 13.2 - - + -
551B LEU* 1.3 76.5 - - - +
553B ILE* 1.3 64.0 + - - +
554B VAL* 3.8 22.2 - - + -
569B ARG 3.8 0.2 - - - +
570B VAL* 3.7 2.9 - - - +
571B LEU* 2.6 45.5 + - + +
573B ILE* 4.1 23.1 - - + -
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Residues in contact with ILE 553 (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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454A VAL* 4.3 4.9 - - + -
459B ALA* 4.0 18.8 - - + -
462B ALA* 3.9 16.8 - - + -
463B ALA* 4.0 17.7 - - + +
466B CYS* 4.3 8.1 - - - -
468B ALA* 3.9 16.4 - - + -
470B ALA 3.0 8.8 + - - +
471B ILE* 3.2 10.7 - - + +
472B ILE* 2.7 33.3 + - - +
552B VAL* 1.3 78.2 - - - +
554B VAL* 1.3 60.0 + - - +
568B MET* 3.7 28.5 - - + -
569B ARG 3.4 2.7 - - - +
570B VAL* 3.9 26.9 - - + -
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Residues in contact with VAL 554 (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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472B ILE* 3.4 13.9 - - + +
474B LEU* 5.6 0.2 - - + -
533B VAL* 3.7 29.2 - - + -
552B VAL* 3.8 15.5 - - + -
553B ILE* 1.3 76.8 - - - +
555B VAL* 1.3 64.6 + - - +
556B THR* 4.0 7.9 + - + -
567B ILE 3.8 0.9 - - - +
568B MET* 3.5 3.8 - - - -
569B ARG* 2.8 65.8 + - + +
571B LEU* 3.6 31.0 - - + -
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Residues in contact with VAL 555 (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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455B THR* 4.2 8.7 - - + -
456B ALA* 5.8 0.9 - - - +
459B ALA* 3.7 30.3 - - + -
471B ILE* 4.0 14.6 - - + -
472B ILE 2.8 10.7 + - - +
473B VAL* 3.5 20.5 - - + +
474B LEU 3.3 25.3 + - - +
480B SER* 5.4 0.7 - - - -
484B LEU* 4.5 6.7 - - + -
553B ILE* 4.6 0.4 - - + -
554B VAL* 1.3 76.1 - - - +
556B THR* 1.3 64.6 + - - +
565B THR* 3.4 31.2 - - + -
567B ILE 3.3 10.1 - - - +
568B MET* 4.6 3.4 - - + -
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Residues in contact with THR 556 (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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474B LEU* 3.8 28.5 - - + -
529B VAL* 4.1 16.8 - - + +
533B VAL* 4.2 3.6 - - + -
554B VAL* 4.0 19.6 + - + -
555B VAL* 1.3 79.1 - - - +
557B GLY* 1.3 62.4 + - - +
565B THR* 3.3 11.9 - - - +
566B ASN 3.0 20.4 + - - -
567B ILE* 3.1 34.4 + - - +
569B ARG* 4.3 10.3 + - - +
580B FBP 4.1 7.2 - - - -
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Residues in contact with GLY 557 (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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525B TRP* 3.3 15.1 - - - -
529B VAL* 5.6 1.2 - - - +
556B THR* 1.3 83.5 + - - +
558B TRP* 1.3 63.5 + - - -
564B TYR 3.7 11.4 - - - -
565B THR* 4.0 0.7 - - - -
566B ASN* 3.9 4.3 - - - -
567B ILE* 3.7 12.3 - - - +
580B FBP 2.8 25.6 + - - -
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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