Contacts of the strand formed by residues 317 - 322 (chain B) 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 ASP 317 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269B CYS* 3.7 15.5 - - + +
270B TRP 3.5 15.8 - - - +
271B GLN* 4.7 3.9 - - - +
272B ALA 4.4 1.8 - - - +
310B GLU* 5.1 5.7 - - - +
315B SER* 3.5 14.5 + - - +
316B GLN* 1.3 84.8 + - - +
318B ASP* 1.3 72.3 + - - +
319B CYS* 3.8 20.2 + - - -
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Residues in contact with ASP 318 (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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269B CYS* 3.3 1.4 - - - -
270B TRP* 2.8 34.9 + - + +
272B ALA* 3.8 12.4 - - - +
273B GLY* 3.2 23.3 + - - -
275B THR* 3.9 12.7 + - - +
316B GLN 4.5 0.3 - - - +
317B ASP* 1.3 82.1 - - - +
319B CYS* 1.3 61.2 + - - +
320B TYR* 3.3 32.1 + - + +
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Residues in contact with CYS 319 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267B LEU* 4.8 11.4 - - + -
268B VAL 3.2 2.5 - - - -
269B CYS* 2.0 46.2 - - - -
308B PRO* 3.4 6.4 - - - +
309B VAL* 2.8 42.7 + - - +
315B SER* 5.4 3.8 - - - -
317B ASP* 3.8 15.4 + - - -
318B ASP* 1.3 73.3 - - - +
320B TYR* 1.3 65.4 + - - +
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Residues in contact with TYR 320 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261B PHE* 4.6 0.5 - - - -
267B LEU* 3.2 13.6 - - - +
268B VAL* 2.8 41.9 + - + +
270B TRP* 3.4 20.9 - + + -
275B THR* 3.4 31.0 + - + -
277B TRP* 3.5 29.1 - + - -
306B LEU* 3.6 36.3 - - + -
307B ARG 3.1 4.0 - - - +
308B PRO* 3.7 23.1 - - + -
309B VAL* 5.2 0.4 - - - -
318B ASP* 3.3 35.1 + - + +
319B CYS* 1.3 79.5 - - - +
321B LYS* 1.3 60.8 + - - +
322B PHE 4.3 0.5 + - - -
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Residues in contact with LYS 321 (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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233B ASN* 4.7 19.8 + - - +
261B PHE* 4.8 0.4 - - - -
264B GLY* 3.3 35.2 - - - +
266B GLN 5.7 0.7 - - - +
267B LEU* 3.8 19.5 - - + +
306B LEU* 3.4 6.9 - - - -
307B ARG* 2.6 47.1 + - + +
309B VAL* 4.5 9.1 - - + +
320B TYR* 1.3 75.2 - - - +
322B PHE* 1.3 68.8 + - - +
323B ALA* 3.2 6.1 + - - +
1000B 757 4.8 10.9 - - - +
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Residues in contact with PHE 322 (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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233B ASN* 4.8 1.4 + - - -
241B PHE* 4.2 0.7 - + - -
245B VAL* 4.2 14.1 - - + -
248B ILE* 3.9 18.6 - - + -
261B PHE* 3.4 42.9 + + + +
262B TRP* 3.4 52.3 - + - -
264B GLY* 4.2 8.4 + - - -
266B GLN 5.8 0.2 + - - -
280B PHE* 6.2 0.2 - + - -
305B TYR* 3.9 24.7 - + - -
306B LEU* 3.9 19.3 - - + -
321B LYS* 1.3 79.7 - - - +
323B ALA* 1.3 60.0 + - - +
324B ILE* 3.2 47.1 + - + +
325B SER* 5.7 0.3 - - - -
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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