Contacts of the strand formed by residues 565 - 572 (chain A) 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 THR 565 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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451A PRO* 3.9 4.0 - - - +
452A THR* 3.7 41.6 + - + +
455A THR* 4.3 7.6 - - - -
473A VAL* 5.4 0.2 - - + -
474A LEU 4.5 2.4 + - - -
480A SER* 3.0 23.4 + - - -
555A VAL* 3.4 27.4 - - + -
556A THR* 3.3 17.5 + - - +
557A GLY* 4.0 2.9 - - - -
563A GLY 3.7 2.5 - - - +
564A TYR* 1.3 77.8 - - - +
566A ASN* 1.3 69.8 + - - +
580A FBP 3.4 17.5 + - - -
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Residues in contact with ASN 566 (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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451A PRO* 4.3 9.9 - - + -
455A THR* 3.3 19.0 - - - +
556A THR 3.1 4.8 + - - -
558A TRP* 3.3 37.4 + - + +
564A TYR 3.9 0.9 - - - +
565A THR* 1.3 78.4 - - - +
567A ILE* 1.3 75.4 + - - +
569B ARG* 3.3 6.1 - - - +
570B VAL* 2.6 52.3 + - + +
571B LEU* 3.7 16.6 - - - +
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Residues in contact with ILE 567 (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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455A THR* 3.5 8.4 - - - +
554A VAL 4.4 0.4 - - - +
555A VAL* 3.3 6.8 - - - +
556A THR* 3.1 43.2 + - - +
557A GLY 3.7 26.9 - - - +
558A TRP* 4.1 6.7 - - + +
566A ASN* 1.3 95.8 - - - +
568A MET* 1.3 63.8 + - - +
569A ARG* 4.0 25.1 - - + -
567B ILE* 4.1 4.3 - - + -
568B MET 3.6 3.8 - - - +
569B ARG* 3.9 29.4 - - + -
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Residues in contact with MET 568 (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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455A THR* 4.0 11.9 - - + +
458A GLY 4.1 5.6 - - - +
459A ALA* 3.9 29.4 - - + +
462A ALA* 4.0 16.4 - - + -
553A ILE* 3.7 17.7 - - + -
554A VAL 3.5 3.4 - - - +
555A VAL* 4.6 0.4 - - + -
567A ILE* 1.3 76.0 - - - +
569A ARG* 1.3 69.0 + - - +
570A VAL* 3.7 30.3 - - + +
455B THR* 4.8 9.0 - - + -
458B GLY* 5.2 4.3 - - - -
566B ASN 4.8 2.5 - - - +
567B ILE* 3.5 0.5 - - - +
568B MET* 2.8 61.2 + - + +
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Residues in contact with ARG 569 (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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529A VAL* 5.2 2.4 - - - +
530A ASP* 4.5 12.8 + - - -
533A VAL* 4.2 13.1 - - - +
553A ILE* 3.4 5.7 - - - +
554A VAL* 2.8 63.7 + - + +
556A THR* 4.2 17.2 + - - +
567A ILE* 4.0 9.9 - - + +
568A MET* 1.3 82.2 - - - +
570A VAL* 1.3 66.6 + - - +
571A LEU* 3.7 34.5 + - + +
558B TRP* 6.6 0.2 - - - -
566B ASN* 3.5 7.4 - - - +
567B ILE* 3.8 31.9 - - + -
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Residues in contact with VAL 570 (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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466A CYS* 5.5 0.4 - - - -
551A LEU* 4.2 28.0 - - + -
552A VAL 3.7 6.1 - - - +
553A ILE* 3.8 16.4 - - + -
568A MET* 3.7 21.8 - - + -
569A ARG* 1.3 72.3 - - - +
571A LEU* 1.3 63.4 + - - +
451B PRO* 4.4 20.3 - - + +
454B VAL* 4.1 19.1 - - + -
455B THR* 4.2 12.6 - - - +
566B ASN* 2.5 45.0 + - + +
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Residues in contact with LEU 571 (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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533A VAL* 4.6 9.6 - - + -
534A GLN* 5.6 3.4 - - - +
537A ILE* 4.9 10.8 - - + -
551A LEU* 3.4 7.8 - - - +
552A VAL* 2.6 48.4 + - + +
554A VAL* 3.6 28.7 - - + -
569A ARG* 3.7 30.5 - - + +
570A VAL* 1.3 83.7 - - - +
572A SER* 1.3 62.4 + - - +
573A ILE* 5.6 1.1 - - + -
558B TRP* 6.1 3.4 - - + -
566B ASN* 4.2 9.2 - - - +
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Residues in contact with SER 572 (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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537A ILE* 6.0 0.2 - - - +
549A GLY* 5.4 3.8 - - - -
550A ASP 3.4 8.1 - - - -
551A LEU* 3.8 16.8 - - - +
571A LEU* 1.3 77.4 - - - +
573A ILE* 1.3 69.3 + - - +
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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