Contacts of the strand formed by residues 551 - 557 (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 LEU 551 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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466A CYS* 3.6 43.3 - - + +
467A CYS 5.7 0.8 + - - -
468A ALA* 3.6 3.2 - - - +
469A ALA 3.3 24.7 + - - +
549A GLY 3.8 2.2 + - - +
550A ASP* 1.3 78.3 - - - +
552A VAL* 1.3 62.6 + - - +
570A VAL* 4.2 17.9 - - + -
571A LEU 3.4 13.9 - - - +
572A SER* 3.8 20.4 - - - -
449B ARG* 4.0 45.9 - - + +
451B PRO* 5.1 7.9 - - + -
454B VAL* 5.3 1.6 - - + -
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Residues in contact with VAL 552 (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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468A ALA* 4.6 1.1 - - - -
469A ALA* 5.4 0.2 - - + -
470A ALA* 3.1 39.7 - - + +
472A ILE* 4.1 20.0 - - + -
537A ILE* 5.0 0.9 - - + -
546A LEU* 4.5 11.4 - - + -
551A LEU* 1.3 77.9 - - - +
553A ILE* 1.3 63.6 + - - +
554A VAL* 3.8 23.1 + - + -
570A VAL* 3.7 2.9 - - - +
571A LEU* 2.6 46.7 + - + +
573A ILE* 4.0 22.0 - - + -
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Residues in contact with ILE 553 (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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459A ALA* 4.0 17.5 - - + -
462A ALA* 3.9 18.6 - - + +
463A ALA* 4.0 26.9 - - + +
466A CYS* 4.5 10.3 - - - -
468A ALA* 4.0 7.4 - - + -
470A ALA 3.0 8.5 + - - +
471A ILE* 3.2 10.5 - - + +
472A ILE* 2.7 32.4 + - - +
552A VAL* 1.3 78.8 - - - +
554A VAL* 1.3 60.4 + - - +
555A VAL* 4.1 0.9 - - + -
568A MET* 3.7 29.4 - - + -
569A ARG 3.4 3.8 - - - +
570A VAL* 3.8 27.1 - - + -
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Residues in contact with VAL 554 (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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472A ILE* 3.4 14.8 - - + +
474A LEU* 5.6 0.2 - - + -
533A VAL* 3.7 30.1 - - + -
537A ILE* 5.7 0.2 - - + -
552A VAL* 3.8 15.0 - - + -
553A ILE* 1.3 76.3 - - - +
555A VAL* 1.3 63.8 + - - +
556A THR* 3.9 7.9 + - + +
567A ILE* 3.8 0.9 - - - +
568A MET* 3.5 2.3 - - - -
569A ARG* 2.8 69.8 + - - +
571A LEU* 3.6 29.8 - - + -
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Residues in contact with VAL 555 (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* 4.1 9.0 - - + -
456A ALA* 5.8 0.9 - - - +
459A ALA* 3.7 30.1 - - + -
471A ILE* 3.9 15.3 - - + -
472A ILE 2.8 10.5 + - - +
473A VAL* 3.4 22.6 - - + +
474A LEU 3.3 23.7 + - - +
480A SER* 5.4 0.9 - - - -
484A LEU* 4.5 6.1 - - + -
553A ILE* 4.5 2.0 - - + -
554A VAL* 1.3 75.9 - - - +
556A THR* 1.3 67.4 + - - +
565A THR* 3.4 28.7 - - + -
567A ILE 3.3 10.1 - - - +
568A MET* 4.6 2.7 - - + -
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Residues in contact with THR 556 (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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474A LEU* 3.9 23.6 - - + -
529A VAL* 4.2 13.2 - - + +
533A VAL* 4.2 7.2 - - + -
554A VAL* 3.9 21.2 + - + -
555A VAL* 1.3 79.7 - - - +
557A GLY* 1.3 62.1 + - - +
565A THR* 3.3 11.1 - - - +
566A ASN 3.1 19.4 + - - -
567A ILE* 3.1 34.3 + - - +
569A ARG* 4.2 10.7 + - - +
580A FBP 4.1 10.5 - - - -
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Residues in contact with GLY 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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525A TRP* 3.3 14.9 - - - -
529A VAL* 5.6 1.4 - - - +
556A THR* 1.3 83.1 + - - +
558A TRP* 1.3 63.9 + - - -
559A ARG 3.4 2.9 - - - -
564A TYR 3.6 11.9 - - - -
565A THR* 4.0 1.3 - - - -
566A ASN* 3.9 3.8 - - - -
567A ILE* 3.7 13.2 - - - +
580A FBP 3.0 21.7 + - - -
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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