Contacts of the strand formed by residues 305 - 310 (chain A) in PDB entry 3ZDY
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 305 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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244A PHE* 4.4 2.9 - - - -
294A ALA 3.9 0.2 - - - +
295A VAL* 3.5 7.8 - - - +
296A THR* 3.1 35.4 + - - +
297A ASP* 3.2 2.3 - - - +
298A VAL* 3.0 25.0 + - + -
299A ASN* 3.2 16.5 - - - +
301A ASP* 4.8 0.9 - - - +
303A ARG 3.1 12.6 - - - +
304A HIS* 1.3 73.8 - - - +
306A LEU* 1.3 62.3 + - - +
307A LEU* 5.8 0.7 - - - -
330A LEU* 4.4 8.3 - - + -
331A PHE 3.4 10.1 - - - +
332A LEU* 3.3 23.6 - - + +
333A GLN* 3.0 23.8 + - - +
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Residues in contact with LEU 306 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244A PHE* 4.5 12.7 - - + -
254A VAL* 3.7 29.6 - - + -
267A VAL* 4.3 6.5 - - + -
269A ILE* 4.7 6.3 - - + -
280A LEU* 3.0 36.3 - - + -
293A VAL* 4.7 2.2 - - + -
294A ALA 3.7 9.4 - - - +
295A VAL* 4.5 7.2 - - + -
305A ASP* 1.3 74.3 - - - +
307A LEU* 1.3 73.7 + - - +
308A VAL* 4.0 15.9 - - + -
329A TYR 3.7 0.7 - - - +
330A LEU* 3.6 5.2 - - - +
331A PHE* 2.8 47.7 + - + +
340A LEU* 4.6 9.2 - - + -
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Residues in contact with LEU 307 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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292A SER 4.0 0.2 - - - +
293A VAL* 3.4 5.9 - - - -
294A ALA* 2.9 45.3 + - + +
296A THR* 4.4 14.8 - - + +
298A VAL* 4.8 5.2 - - + -
305A ASP 5.7 0.9 - - - +
306A LEU* 1.3 78.1 - - - +
308A VAL* 1.3 63.1 + - - +
328A VAL* 3.8 17.5 - - + -
329A TYR 3.3 14.8 - - - +
330A LEU* 4.0 24.2 - - + -
347A LEU* 6.0 0.4 - - + -
360A ILE* 4.0 15.8 - - + +
374A ILE* 3.7 45.1 - - + -
399A LEU* 4.2 4.7 - - + -
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Residues in contact with VAL 308 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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267A VAL* 3.8 23.1 - - + -
289A PHE* 3.5 33.9 - - + -
290A GLY* 3.6 23.1 - - - +
292A SER 3.6 3.1 - - - +
293A VAL* 4.6 1.8 - - + -
306A LEU* 4.0 24.0 - - + -
307A LEU* 1.3 79.6 - - - +
309A GLY* 1.3 61.4 + - - +
328A VAL* 3.3 3.8 - - - -
329A TYR* 2.8 40.4 + - + +
331A PHE* 4.0 13.7 - - + -
360A ILE* 3.9 3.6 - - - -
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Residues in contact with GLY 309 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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288A TYR 3.4 3.5 - - - +
290A GLY 3.2 21.7 + - - -
291A HIS 3.4 6.9 + - - -
292A SER* 3.0 16.6 + - - -
308A VAL* 1.3 73.8 - - - +
310A ALA* 1.3 60.5 + - - -
311A PRO* 3.7 5.3 - - - +
327A ARG 3.7 4.3 - - - -
328A VAL* 4.5 2.2 - - - -
357A GLY 3.6 17.7 - - - -
360A ILE* 3.6 8.8 - - - +
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Residues in contact with ALA 310 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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287A SER* 3.4 21.8 - - - +
288A TYR 3.8 1.6 - - - -
289A PHE* 3.7 17.7 - - + +
308A VAL 4.1 0.2 + - - -
309A GLY* 1.3 72.6 - - - -
311A PRO* 1.3 67.9 - - - +
312A LEU 3.0 5.2 + - - -
313A TYR* 3.1 9.7 + - + +
327A ARG 2.8 33.3 + - - +
329A TYR* 4.0 19.1 - - + +
357A GLY 4.3 0.6 + - - -
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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
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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