Contacts of the strand formed by residues 305 - 311 (chain A) in PDB entry 2YD0
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 LYS 305 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216A ILE* 5.3 0.4 - - - +
217A SER 2.8 25.3 + - - +
218A ASN 3.4 13.8 + - - +
219A MET 3.6 17.3 - - - -
220A PRO* 3.8 24.7 - - + -
265A VAL* 3.8 6.1 - - - -
266A LYS* 3.2 23.8 - - + +
301A TYR* 3.1 17.7 + - - -
303A LEU* 3.2 6.5 - - - +
304A PRO* 1.3 80.0 - - + +
306A GLN* 1.3 59.3 + - - +
307A ASP* 2.8 33.4 + - - +
323A GLY* 2.8 19.6 + - - +
324A LEU* 4.5 0.4 - - - +
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Residues in contact with GLN 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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265A VAL* 3.8 6.8 - - + +
266A LYS 2.8 8.0 + - - +
267A VAL* 3.2 14.3 - - + +
268A SER 2.9 23.7 + - - -
290A LEU* 4.9 5.4 - - + -
301A TYR* 2.8 32.1 + - + +
305A LYS* 1.3 72.3 - - - +
307A ASP* 1.3 92.1 + - - +
308A LEU* 4.3 10.5 - - + -
323A GLY 3.2 16.1 + - - -
325A THR* 3.3 21.4 - - - +
355A LEU* 4.0 20.4 - - + -
358A GLN* 2.9 23.4 - - - +
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Residues in contact with ASP 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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216A ILE* 4.5 9.5 - - - +
266A LYS 4.6 1.0 - - - +
268A SER* 3.3 21.2 + - - +
270A TYR* 3.6 28.4 + - + -
305A LYS* 2.8 32.8 + - - +
306A GLN* 1.3 85.2 + - - +
308A LEU* 1.3 62.5 + - - +
309A ALA 4.0 0.4 - - - -
323A GLY 3.0 12.2 + - - +
324A LEU* 3.9 13.9 - - + -
325A THR* 2.8 27.2 + - - -
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Residues in contact with LEU 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* 3.7 25.6 - - + -
268A SER 2.7 18.7 + - - +
269A VAL* 3.1 19.0 - - + +
270A TYR* 2.9 22.1 + - - -
282A ALA 4.9 2.9 - - - +
286A ALA* 3.9 20.4 - - + -
306A GLN* 4.3 9.9 - - + -
307A ASP* 1.3 78.2 - - - +
309A ALA* 1.3 58.3 + - - +
325A THR* 3.3 16.2 - - - +
327A TYR* 3.3 26.7 - - + +
332A LEU* 4.1 16.4 - - + -
351A VAL* 4.1 13.0 - - + -
355A LEU* 5.2 3.1 - - + -
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Residues in contact with ALA 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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216A ILE* 4.9 1.6 - - + -
250A ILE* 3.8 28.9 - - + -
254A PHE* 4.5 3.6 - - + -
270A TYR* 3.5 17.0 - - + -
307A ASP 4.0 0.4 - - - -
308A LEU* 1.3 71.2 - - - +
310A ALA* 1.3 61.2 + - - +
311A ILE* 3.4 8.1 + - + +
324A LEU* 4.2 8.5 - - + -
325A THR 2.9 14.8 + - - +
326A THR* 3.5 3.0 - - + -
327A TYR* 3.0 26.4 + - - -
332A LEU* 4.0 3.8 - - - -
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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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254A PHE* 3.4 20.3 - - - -
270A TYR 2.8 17.5 + - - +
271A ALA* 4.1 6.2 - - + -
272A VAL 5.1 0.3 + - - -
309A ALA* 1.3 71.2 - - - +
311A ILE* 1.3 62.7 + - - +
312A PRO* 3.7 2.6 - - - +
327A TYR 3.6 4.9 - - - -
329A GLU* 4.1 15.6 - - + +
332A LEU* 3.9 17.8 - - + +
333A LEU* 3.9 31.6 - - + -
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Residues in contact with ILE 311 (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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163A TYR* 4.0 6.5 - - - +
165A SER* 3.9 6.7 - - - +
177A LEU* 4.3 3.8 - - + -
179A SER* 3.8 20.6 - - - +
250A ILE* 3.7 30.7 - - + -
254A PHE* 4.3 8.3 - - + -
309A ALA* 3.9 17.3 - - + +
310A ALA* 1.3 75.5 - - - +
312A PRO* 1.3 74.8 - - + +
313A ASP 3.2 19.0 + - - +
314A PHE* 4.0 25.5 - - + +
326A THR* 4.1 10.3 - - + -
327A TYR 2.8 18.7 + - - +
328A ARG* 4.2 3.5 - - - -
329A GLU* 3.7 13.2 + - - +
830A GLN* 4.8 1.0 + - - +
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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