Contacts of the strand formed by residues 306 - 308 (chain C) in PDB entry 3DM6
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 306 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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261C PHE* 3.9 16.2 - - + -
270C TRP* 4.3 16.8 - - + -
275C THR* 5.4 0.4 - - + -
277C TRP* 4.0 21.8 - - + -
280C PHE* 3.7 39.0 - - + -
302C PRO* 2.7 19.5 + - + +
303C GLN 4.3 5.7 - - - +
304C GLN 4.9 0.2 - - - -
305C TYR* 1.3 90.4 - - + +
307C ARG* 1.3 62.5 + - - +
308C PRO* 3.7 4.5 - - - +
320C TYR* 3.6 20.4 - - + -
321C LYS 3.3 5.6 - - - +
322C PHE* 3.7 29.4 - - + -
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Residues in contact with ARG 307 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10C SER* 4.9 7.9 + - - +
11C GLY* 4.2 18.2 - - - +
14C TYR* 4.4 3.6 + - - -
156C GLY* 5.5 1.0 - - - -
170C VAL* 5.4 2.6 - - - +
232C THR* 3.5 28.5 - - - +
303C GLN 5.8 0.9 - - - +
304C GLN 4.4 13.0 + - - +
305C TYR 3.6 0.4 - - - -
306C LEU* 1.3 72.9 - - - +
308C PRO* 1.4 74.5 - - + +
309C VAL* 3.6 1.2 + - + +
320C TYR* 3.3 1.9 - - - -
321C LYS* 2.7 51.1 + - + +
323C ALA* 3.9 20.4 - - + -
335C ALA* 4.4 9.4 + - - -
336C VAL* 4.7 1.7 - - - +
339C GLU* 2.6 45.8 + - - -
1000C 757 4.1 22.8 - - - -
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Residues in contact with PRO 308 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10C SER* 4.3 21.8 + - - +
157C ALA* 3.8 30.1 - - + -
303C GLN 5.5 2.0 - - - +
306C LEU 3.7 6.0 - - - +
307C ARG* 1.4 93.6 - - + +
309C VAL* 1.3 63.4 + - - +
310C GLU 4.2 0.8 + - - -
319C CYS 3.4 7.9 - - - +
320C TYR* 3.8 16.6 - - + -
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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
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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