Contacts of the strand formed by residues 549 - 555 (chain B) in PDB entry 3NG8
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 ILE 549 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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556A GLN* 4.4 3.5 - - - +
474B ILE* 3.8 23.3 - - + -
475B VAL 3.7 2.5 - - - -
476B THR* 4.9 0.4 - - + -
489B LEU* 4.3 6.5 - - + -
534B ALA 5.3 0.4 - - - +
538B LYS* 3.0 51.1 + - + -
541B LEU* 3.7 42.2 - - + -
542B GLU* 2.9 16.8 + - + +
547B LEU* 4.0 12.8 - - + -
548B GLN* 1.3 73.2 - - - +
550B LEU* 1.3 64.8 + - - +
551B GLN 3.9 4.5 - - - +
552B THR* 3.6 30.3 - - + -
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Residues in contact with LEU 550 (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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471A TYR* 4.7 0.7 + - - -
555A GLY* 3.1 3.4 - - - -
556A GLN* 2.9 45.9 + - + +
475B VAL* 2.8 20.5 + - + +
476B THR 3.6 27.4 - - - +
477B ASP* 4.1 10.3 - - + -
479B LYS* 6.3 2.0 - - - -
538B LYS* 5.1 0.7 - - - -
548B GLN* 4.4 16.4 - - + -
549B ILE* 1.3 79.5 - - - +
551B GLN* 1.3 66.3 + - + +
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Residues in contact with GLN 551 (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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471A TYR* 4.5 8.4 + - - +
473A TYR* 3.0 39.2 + - + +
475A VAL* 5.8 0.3 - - - +
551A GLN* 4.2 5.7 - - - +
554A VAL 3.3 7.9 - - - -
555A GLY* 4.4 2.2 - - - -
473B TYR* 4.0 4.4 + - + -
474B ILE* 3.4 0.2 - - - -
475B VAL* 2.8 61.7 + - + +
538B LYS* 6.1 0.2 - - - +
549B ILE* 3.7 2.0 - - - +
550B LEU* 1.3 87.3 - - + +
552B THR* 1.3 70.7 + - - +
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Residues in contact with THR 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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473A TYR* 4.2 2.7 - - - -
553A GLY* 3.2 1.7 - - - -
554A VAL* 2.9 38.3 + - - +
473B TYR* 3.3 7.4 - - - -
474B ILE* 3.9 18.6 - - + -
531B THR* 4.2 21.5 + - - -
534B ALA* 4.4 17.3 - - + +
535B GLY* 4.8 6.3 + - - -
538B LYS* 5.8 0.9 - - + -
549B ILE* 3.6 21.8 - - + -
551B GLN* 1.3 80.9 - - - +
553B GLY* 1.3 58.4 + - - +
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Residues in contact with GLY 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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552A THR 3.2 13.2 - - - -
553A GLY* 3.8 1.8 - - - -
472B GLY* 3.4 4.5 - - - -
473B TYR* 2.9 46.3 + - - +
531B THR* 3.5 13.3 - - - +
552B THR* 1.3 77.1 - - - +
554B VAL* 1.3 64.6 + - - -
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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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535A GLY* 6.5 1.1 - - - -
551A GLN* 3.3 2.9 - - - +
552A THR* 2.9 39.0 + - - +
470B GLU* 3.7 37.0 - - + +
471B TYR 3.2 12.1 - - - +
472B GLY* 4.7 0.4 - - - -
473B TYR* 3.5 3.3 - - - -
527B LEU* 4.2 22.9 - - + +
528B ALA* 4.7 4.3 - - - +
531B THR* 4.2 17.0 - - + +
553B GLY* 1.3 79.0 - - - +
555B GLY* 1.3 65.0 + - - +
556B GLN* 4.1 7.0 + - - +
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Residues in contact with GLY 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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550A LEU 3.3 10.8 - - - -
551A GLN* 4.2 4.5 - - - -
470B GLU* 3.3 5.7 - - - +
471B TYR* 2.8 54.7 + - - -
473B TYR* 3.8 4.4 - - - -
554B VAL* 1.3 77.8 - - - +
556B GLN* 1.3 64.9 + - - -
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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