Contacts of the helix formed by residues 537 - 546 (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 VAL 537 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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492B ILE* 5.3 0.2 - - + -
493B LEU* 4.5 7.6 - - + -
496B HIS* 3.4 47.1 - - + +
533B GLN* 3.0 34.9 + - - +
534B ALA* 3.7 1.3 - - - -
536B LEU* 1.3 79.5 - - + +
538B LYS* 1.3 64.5 + - - +
539B SER 3.2 3.1 - - - -
540B GLU* 3.0 23.1 + - + +
541B LEU* 2.9 39.8 + - + +
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Residues in contact with LYS 538 (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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470A GLU* 4.2 22.1 + - + +
554A VAL* 5.7 1.6 + - - +
555A GLY* 4.9 2.2 - - - -
556A GLN* 3.5 28.1 + - - +
534B ALA 3.1 12.5 + - - +
535B GLY* 3.2 17.9 + - - +
536B LEU 3.4 1.4 + - - -
537B VAL* 1.3 76.5 - - - +
539B SER* 1.3 59.8 + - - +
541B LEU* 3.3 7.1 + - - +
542B GLU* 2.9 44.6 + - - +
549B ILE* 3.0 50.2 + - + +
550B LEU 5.1 1.4 + - - -
551B GLN* 6.1 0.2 - - - +
552B THR* 5.8 0.9 - - - -
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Residues in contact with SER 539 (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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536B LEU 5.2 0.2 + - - -
537B VAL 3.2 1.0 - - - -
538B LYS* 1.3 79.8 - - - +
540B GLU* 1.3 66.3 + - - +
542B GLU* 3.5 9.1 + - - +
543B ALA* 2.9 30.1 + - - +
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Residues in contact with GLU 540 (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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492B ILE* 5.0 1.6 - - + -
496B HIS* 4.3 13.8 + - + -
536B LEU 4.1 4.2 - - - +
537B VAL* 3.0 42.3 + - + +
539B SER* 1.3 84.5 + - - +
541B LEU* 1.3 64.2 + - - +
543B ALA* 3.9 4.4 - - - -
544B GLN* 3.0 47.6 + - - +
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Residues in contact with LEU 541 (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 ILE* 4.9 5.2 - - + -
489B LEU* 3.7 28.9 - - + +
492B ILE* 3.5 35.0 - - + -
493B LEU* 4.3 7.4 - - + +
534B ALA* 3.6 40.8 - - + +
537B VAL* 2.9 20.9 + - + +
538B LYS* 3.6 5.8 - - - +
540B GLU* 1.3 76.2 - - - +
542B GLU* 1.3 55.2 + - - +
544B GLN 4.0 0.2 - - - -
545B THR* 2.7 37.9 + - - +
549B ILE* 3.7 25.1 - - + -
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Residues in contact with GLU 542 (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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1B CA 2.4 32.0 - - - -
538B LYS* 2.9 29.0 + - - +
539B SER* 3.8 7.6 - - - +
541B LEU* 1.3 76.4 - - - +
543B ALA* 1.3 56.8 + - - +
545B THR* 4.0 1.1 - - - -
546B GLY* 2.9 32.2 + - - -
547B LEU* 3.3 20.1 - - - +
548B GLN* 3.2 16.5 + - - +
549B ILE* 2.9 40.5 + - + +
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Residues in contact with ALA 543 (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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539B SER 2.9 22.5 + - - +
540B GLU* 3.9 5.6 - - - +
542B GLU* 1.3 74.3 - - - +
544B GLN* 1.3 64.5 + - + +
545B THR 3.7 0.2 + - - -
546B GLY* 4.2 3.6 + - - -
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Residues in contact with GLN 544 (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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488B LYS* 2.9 30.9 + - - -
492B ILE* 3.6 36.8 - - + +
496B HIS* 5.3 3.0 - - - -
540B GLU* 3.0 37.9 + - - +
543B ALA* 1.3 81.8 - - + +
545B THR* 1.3 60.7 + - - +
546B GLY 3.7 0.2 - - - -
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Residues in contact with THR 545 (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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485B ALA* 4.8 6.5 - - - +
488B LYS* 4.2 17.5 - - + +
489B LEU* 3.8 22.6 - - + +
492B ILE* 3.8 16.4 - - + -
541B LEU 2.7 22.2 + - - +
542B GLU 3.7 0.2 + - - -
544B GLN* 1.3 81.5 - - - +
546B GLY* 1.3 63.1 + - - +
547B LEU* 3.1 37.5 + - - +
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Residues in contact with GLY 546 (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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477B ASP* 5.3 0.7 - - - +
478B GLN* 4.4 4.9 - - - +
542B GLU 2.9 12.3 + - - -
543B ALA 4.2 3.8 + - - -
544B GLN 3.7 0.8 - - - -
545B THR* 1.3 77.0 - - - +
547B LEU* 1.3 61.3 + - - +
548B GLN* 5.8 0.9 - - - -
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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