Contacts of the strand formed by residues 298 - 304 (chain A) in PDB entry 4UC5
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 ILE 298 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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56A LEU* 4.0 13.1 - - + +
248A VAL* 4.3 11.9 - - + -
263A LYS* 5.3 2.2 - - - +
264A LEU* 3.6 5.8 - - + +
266A ILE* 3.9 26.9 - - + -
287A ILE* 4.3 16.6 - - + -
290A GLN* 3.5 32.8 - - + +
291A LEU* 4.4 6.7 - - + -
295A GLY* 3.3 23.2 + - - +
296A GLY 4.7 0.7 - - - +
297A ASN* 1.3 79.8 - - - +
299A MET* 1.3 60.0 + - - +
300A GLY 3.8 21.1 - - - +
346A ARG* 2.8 30.8 + - - -
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Residues in contact with MET 299 (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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45A ILE* 4.8 1.8 - - + +
48A LEU* 3.6 35.9 - - + +
49A VAL* 4.0 25.1 - - + -
53A ASP 6.0 0.7 - - - +
55A ARG 4.2 5.3 - - - +
56A LEU* 3.9 8.3 - - - -
57A LEU* 3.0 41.2 + - + +
232A HIS* 4.3 13.5 - - - +
263A LYS* 3.6 29.2 - - + +
264A LEU 2.8 24.7 + - - +
265A MET* 4.0 9.0 - - - -
297A ASN 3.9 0.6 + - - -
298A ILE* 1.3 73.0 - - - +
300A GLY* 1.3 64.1 + - - +
346A ARG* 5.2 0.9 - - - +
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Residues in contact with GLY 300 (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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56A LEU* 3.6 7.1 - - - +
57A LEU* 3.0 15.9 - - - -
264A LEU 3.5 0.6 + - - -
265A MET* 3.3 10.8 - - - -
266A ILE 3.0 19.9 + - - -
298A ILE* 3.7 7.5 - - - +
299A MET* 1.3 91.2 - - - +
301A VAL* 1.3 70.0 + - - +
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Residues in contact with VAL 301 (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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56A LEU* 3.6 29.2 - - + -
57A LEU 2.7 10.4 + - - +
58A VAL* 3.4 6.9 - - + +
59A ILE* 2.9 27.4 + - - +
265A MET* 3.9 6.1 - - - +
266A ILE 3.2 8.1 - - - +
268A CYS* 3.3 31.9 - - - -
287A ILE* 4.2 22.2 - - + -
300A GLY* 1.3 80.4 - - - +
302A MET* 1.3 65.4 + - - +
303A VAL* 3.9 10.5 - - + -
339A LEU* 4.3 15.9 - - + -
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Residues in contact with MET 302 (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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59A ILE* 3.3 16.8 - - + +
94A ARG* 3.7 28.9 - - - +
96A TYR* 4.3 6.5 - - - +
161A TRP* 3.6 22.2 - - + -
188A LYS* 3.9 20.0 - - - -
234A ILE* 3.7 18.4 - - + -
265A MET* 3.4 26.2 - - - -
266A ILE 2.9 7.6 + - - +
267A ASP* 3.6 23.8 - - - +
268A CYS* 2.8 26.7 + - - +
301A VAL* 1.3 72.8 - - - +
303A VAL* 1.3 71.5 + - - +
304A GLU* 5.8 1.1 - - + -
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Residues in contact with VAL 303 (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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58A VAL* 4.9 6.3 - - + -
59A ILE 2.9 7.3 + - - +
60A ILE* 3.3 48.1 - - + -
61A GLY 3.3 5.9 + - - +
94A ARG* 4.1 4.5 - - - -
267A ASP* 5.1 0.7 - - - -
268A CYS* 4.1 7.6 - - - -
280A GLN* 3.5 13.2 - - - +
301A VAL* 3.9 16.6 - - + -
302A MET* 1.3 82.7 - - - +
304A GLU* 1.3 67.3 + - - +
327A ILE* 4.0 22.7 - - + -
335A LEU* 4.0 25.8 - - + -
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Residues in contact with GLU 304 (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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61A GLY 3.4 3.4 - - - +
63A CYS* 3.2 19.5 - - - +
94A ARG* 3.1 37.3 + - - +
267A ASP* 5.4 0.9 - - - +
269A SER* 2.8 32.0 + - - +
270A HIS* 3.2 27.6 + - + -
280A GLN* 2.9 28.8 + - - +
302A MET* 5.8 0.7 - - + -
303A VAL* 1.3 73.2 - - - +
305A SER* 1.3 58.0 - - - +
324A ASP* 3.6 16.5 - - - +
325A ALA 4.4 2.9 - - - +
326A CYS* 3.3 14.6 - - + +
327A ILE* 3.2 14.2 + - - +
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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