Contacts of the strand formed by residues 573 - 575 (chain C) in PDB entry 6DBT
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 SER 573 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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556C GLY* 2.9 44.1 + - - -
557C LEU* 4.0 5.2 + - - +
571C THR* 4.0 8.8 + - - -
572C ILE* 1.3 79.0 - - - +
574C ARG* 1.3 76.7 + - - +
575C ARG* 5.8 0.3 - - - +
678C CYS* 5.6 0.7 - - - -
679C LEU 3.1 18.9 + - - -
680C MET* 3.6 17.0 - - - +
693C ILE* 4.0 10.2 - - - +
1006C LEU* 3.7 4.7 - - - -
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Residues in contact with ARG 574 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
553C ILE* 4.5 15.2 - - + +
554C ILE 4.3 2.0 - - - -
555C ASP* 3.7 33.2 - - - +
556C GLY* 3.7 3.8 - - - +
557C LEU* 4.6 10.3 - - - +
572C ILE* 5.2 8.4 - - + +
573C SER* 1.3 84.0 + - - +
575C ARG* 1.3 62.6 + - - +
678C CYS 3.8 0.2 - - - -
679C LEU* 2.9 36.8 + - + +
1003C THR* 2.9 37.5 + - - +
1004C PHE* 4.6 6.5 - - - -
1006C LEU* 3.8 31.2 - - + +
1007C GLU* 4.2 24.9 + - - +
1010C LEU* 4.9 6.3 - - + -
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Residues in contact with ARG 575 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
553C ILE* 3.9 2.1 - - - +
554C ILE* 2.8 51.5 + - + +
556C GLY* 4.3 15.1 + - - +
558C SER* 5.9 4.2 - - - -
573C SER* 5.8 0.2 - - - +
574C ARG* 1.3 78.5 - - - +
576C PHE* 1.3 103.8 + - - +
577C ARG* 3.7 14.1 - - - +
578C TYR* 4.4 3.2 - - - +
677C LEU* 3.3 15.7 - - - +
678C CYS* 3.6 19.1 - - + +
693C ILE* 5.3 7.5 + - - +
696C PRO* 3.8 19.0 - - - +
697C VAL* 4.3 25.7 - - - +
700C GLU* 5.6 3.2 + - - +
1010C LEU* 4.5 6.7 - - - +
169D THR* 3.3 28.7 + - - -
170D GLN* 5.0 1.6 - - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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