Contacts of the helix formed by residues 593 - 601 (chain B) in PDB entry 4DBG
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 GLY 593 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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590B PRO 3.2 5.1 + - - -
591B GLU 3.6 1.0 - - - -
592B GLU* 1.3 77.9 - - - +
594B SER* 1.3 67.2 + - - +
595B LEU 3.2 3.4 - - - -
596B GLN* 3.2 34.6 + - - +
597B ALA* 3.2 15.2 + - - +
612B LEU* 4.0 9.2 - - - +
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Residues in contact with SER 594 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
580B VAL* 4.0 14.2 + - - +
583B LEU* 3.7 15.8 - - - +
588B PHE* 3.0 20.4 + - - +
589B GLY 3.0 29.0 + - - -
590B PRO* 3.5 4.4 - - - -
592B GLU 3.4 3.0 + - - -
593B GLY* 1.3 75.0 - - - +
595B LEU* 1.3 66.4 + - - +
597B ALA* 3.9 1.9 - - - +
598B LEU* 3.1 28.0 + - - +
612B LEU* 4.3 13.9 - - - +
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Residues in contact with LEU 595 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
544B PRO 5.5 0.2 - - - +
545B GLY 3.5 20.6 - - - +
546B LEU* 3.6 20.9 - - - +
547B GLY* 4.0 15.0 - - - +
548B ALA 5.4 0.6 + - - -
576B ARG* 3.5 13.0 + - - +
580B VAL* 3.7 39.3 - - + -
590B PRO* 3.7 27.1 - - + +
593B GLY 3.2 1.2 - - - -
594B SER* 1.3 82.7 - - - +
596B GLN* 1.3 72.8 + - - +
598B LEU* 3.5 2.1 + - + +
599B PHE* 3.1 19.6 + - - +
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Residues in contact with GLN 596 (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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590B PRO 3.9 7.1 - - - +
593B GLY* 3.2 36.5 - - - +
595B LEU* 1.3 83.5 + - - +
597B ALA* 1.3 59.2 + - - +
599B PHE* 3.4 8.5 + - + +
600B GLN* 2.8 34.9 + - - +
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Residues in contact with ALA 597 (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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593B GLY 3.2 15.5 + - - +
594B SER 3.9 0.9 - - - +
596B GLN* 1.3 75.0 - - - +
598B LEU* 1.3 62.2 + - - +
600B GLN* 4.2 10.8 - - - +
601B HIS* 2.9 38.9 + - - +
608B ALA* 4.0 13.6 - - + +
611B GLU* 4.8 6.7 - - + -
612B LEU* 3.7 33.0 - - + -
615B GLN* 5.9 0.7 - - - +
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Residues in contact with LEU 598 (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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553B GLU* 4.1 0.2 - - - +
576B ARG* 4.1 22.9 - - - +
579B LYS* 4.4 11.0 - - + -
580B VAL* 4.2 26.7 - - + -
583B LEU* 3.5 33.2 - - + -
594B SER* 3.1 16.2 + - - +
595B LEU* 3.6 5.6 - - - +
597B ALA* 1.3 77.7 - - - +
599B PHE* 1.3 60.3 + - - +
601B HIS* 3.3 2.2 + - - -
602B GLY 3.3 3.6 + - - -
603B GLY* 2.8 52.6 + - - +
605B VAL* 4.4 12.8 - - + -
608B ALA* 3.9 11.8 - - + +
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Residues in contact with PHE 599 (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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548B ALA* 3.5 40.2 - - + +
549B PHE 3.4 28.3 - - - -
550B SER* 3.5 19.0 - - - -
551B CYS 5.3 0.7 - - - -
552B GLN* 5.2 0.2 - - - +
576B ARG* 4.0 5.0 - - - +
595B LEU 3.1 14.5 + - - +
596B GLN* 3.7 9.2 - - + +
598B LEU* 1.3 75.9 - - - +
600B GLN* 1.3 73.3 + - + +
601B HIS 3.2 0.9 + - - -
602B GLY 3.4 8.3 + - - -
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Residues in contact with GLN 600 (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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596B GLN* 2.8 20.2 + - - +
597B ALA* 3.8 7.9 - - - +
598B LEU 3.1 0.4 - - - -
599B PHE* 1.3 89.8 - - + +
601B HIS* 1.3 89.2 + - + +
602B GLY 3.8 0.7 + - - -
607B ARG* 5.1 1.0 + - - -
611B GLU* 4.3 16.9 + - - +
615B GLN* 5.0 4.0 + - - -
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Residues in contact with HIS 601 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
597B ALA* 2.9 26.0 + - - +
598B LEU 3.7 0.7 - - - +
599B PHE 3.1 0.2 - - - -
600B GLN* 1.3 113.3 + - + +
602B GLY* 1.3 62.1 + - - +
603B GLY 3.3 1.8 - - - -
604B ASP* 3.2 31.9 + - - +
607B ARG* 3.6 58.7 + - + +
608B ALA* 4.2 1.3 - - - +
611B GLU* 3.5 33.1 + - + +
614B ARG* 4.8 5.1 + - - -
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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