Contacts of the strand formed by residues 325 - 332 (chain A) in PDB entry 5D3V
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 TYR 325 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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253A LEU* 5.8 1.8 - - + -
256A HIS* 3.1 20.6 + + + +
257A ILE* 3.6 12.5 - - + -
258A GLU* 2.8 30.8 + - - +
275A GLN* 4.2 9.7 + - - -
290A ALA* 3.9 30.1 - - + -
292A PHE* 3.6 27.9 - + - -
301A CYS* 3.7 20.0 - - + -
302A LYS 3.3 4.3 - - - -
303A ARG* 4.4 17.9 - - + -
304A LYS* 4.0 1.3 - - - +
323A SER* 3.7 1.4 - - - -
324A LEU* 1.3 113.5 + - + +
326A ILE* 1.3 64.7 + - - +
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Residues in contact with ILE 326 (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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258A GLU* 3.7 28.0 - - - +
259A GLY* 5.9 0.9 - - - -
301A CYS* 3.2 4.0 - - - -
302A LYS* 2.7 73.3 + - + +
303A ARG 4.8 0.2 - - - +
304A LYS* 4.3 30.7 - - + +
325A TYR* 1.3 77.6 - - - +
327A PHE* 1.3 73.5 + - - +
328A ARG* 3.5 7.9 - - - +
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Residues in contact with PHE 327 (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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257A ILE* 3.8 9.2 - - + +
258A GLU 2.8 14.7 + - - +
259A GLY* 3.3 30.2 - - - +
260A TRP* 3.7 31.9 - + - -
261A GLU* 3.6 43.1 - - + +
299A VAL* 4.1 13.0 - - + -
301A CYS* 4.0 7.9 - - - -
326A ILE* 1.3 75.1 - - - +
328A ARG* 1.3 75.9 + - - +
329A GLY* 3.6 37.0 - - - -
330A ARG* 3.8 24.2 - - + -
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Residues in contact with ARG 328 (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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261A GLU* 5.2 2.6 - - - +
289A ARG* 3.7 11.6 - - - +
300A TYR* 3.0 21.1 + - + +
302A LYS* 3.6 29.8 - - + +
326A ILE* 3.3 21.1 + - - +
327A PHE* 1.3 93.5 + - - +
329A GLY* 1.3 60.0 + - - +
501A FLC 2.6 68.3 + - - +
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Residues in contact with GLY 329 (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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299A VAL* 3.5 8.0 - - - +
300A TYR* 2.9 52.2 + - - +
327A PHE* 3.6 10.9 - - - -
328A ARG* 1.3 80.4 - - - +
330A ARG* 1.3 60.8 + - - +
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Residues in contact with ARG 330 (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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260A TRP* 3.6 9.1 - - - -
261A GLU* 2.8 32.2 + - - -
262A GLY* 4.2 2.9 - - - -
263A SER* 2.9 49.7 + - - +
268A ILE* 3.5 19.8 - - - +
297A LEU* 3.8 22.7 - - + +
298A LEU 3.1 11.0 - - - +
299A VAL* 4.4 5.4 - - + -
300A TYR* 4.2 2.7 + - - -
327A PHE* 3.8 15.9 - - + -
329A GLY* 1.3 75.5 - - - +
331A ILE* 1.3 68.4 + - - +
363A ASN* 4.4 6.2 + - - -
366A LYS* 5.4 5.2 + - - -
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Residues in contact with ILE 331 (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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297A LEU* 3.4 7.3 - - - +
298A LEU* 2.8 53.4 + - + +
300A TYR* 4.4 11.7 - - + +
330A ARG* 1.3 80.7 - - - +
332A ASN* 1.3 77.0 + - - +
333A THR* 3.3 0.7 + - - -
335A VAL* 4.1 5.8 - - + +
336A MET* 3.9 17.9 - - + -
361A ILE* 4.0 17.0 - - + -
363A ASN* 3.8 35.0 - - + +
370A PHE* 3.9 31.0 - - + -
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Residues in contact with ASN 332 (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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296A ASN* 3.6 15.1 - - - +
297A LEU* 4.1 6.3 - - + +
331A ILE* 1.3 76.5 - - - +
333A THR* 1.3 60.0 + - - +
334A GLU* 2.9 33.2 + - - +
335A VAL* 2.9 38.9 + - + +
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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