Contacts of the strand formed by residues 336 - 341 (chain A) in PDB entry 3U78
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 336 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132A PRO* 3.4 24.0 - - + -
133A SER 3.3 17.5 - - - -
134A ALA* 3.8 16.4 - - + -
136A GLU* 3.9 20.0 + - + +
137A ILE* 3.3 46.6 - - + +
301A PHE 3.3 2.1 - - - +
302A TYR* 3.2 5.6 - - - -
303A LEU* 2.7 52.6 + - + +
305A LYS* 5.3 8.3 - - + -
334A LYS* 3.5 37.8 - - + +
335A CYS* 1.3 72.3 - - - +
337A LYS* 1.3 60.5 + - - +
338A CYS 3.8 0.3 + - - -
352A TRP* 4.8 3.8 - + - -
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Residues in contact with LYS 337 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126A LEU 5.9 0.6 + - - -
127A ARG 5.5 4.6 + - - -
129A ARG 4.6 9.9 + - - -
130A VAL* 5.5 6.6 - - + +
131A PHE* 3.6 39.5 - - + +
132A PRO 3.0 9.6 + - - +
133A SER* 3.8 4.1 + - - -
134A ALA* 2.8 25.3 + - - +
300A ILE* 3.9 27.1 - - + -
301A PHE 3.5 3.4 - - - -
302A TYR* 4.4 9.2 - - + -
335A CYS 3.7 1.2 + - - -
336A TYR* 1.3 71.8 - - - +
338A CYS* 1.3 60.3 + - - +
339A VAL* 4.2 22.1 + - + +
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Residues in contact with CYS 338 (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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134A ALA* 3.4 22.2 - - + -
138A ILE* 4.4 12.8 - - - -
161A MET* 4.0 26.5 - - - -
300A ILE* 3.4 1.6 - - - -
301A PHE* 2.7 40.8 + - + +
303A LEU* 3.7 17.7 - - + -
337A LYS* 1.3 72.2 - - - +
339A VAL* 1.3 62.2 + - - +
340A VAL* 3.5 4.5 + - - +
346A LEU* 4.1 19.5 - - - -
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Residues in contact with VAL 339 (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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161A MET* 4.4 8.3 - - - +
298A GLU* 3.7 36.3 - - + +
299A LYS 3.8 3.8 - - - +
300A ILE* 4.3 11.4 - - + +
337A LYS* 4.2 27.3 + - + +
338A CYS* 1.3 73.3 - - - +
340A VAL* 1.3 60.7 + - - +
341A LYS* 3.6 25.1 + - + +
344A HIS* 5.6 1.7 - - - -
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Residues in contact with VAL 340 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161A MET* 4.1 11.9 - - + -
292A TYR* 5.0 3.8 - - + +
294A VAL* 3.1 31.2 - - + +
298A GLU* 3.7 3.3 - - - -
299A LYS 2.8 34.9 + - - +
301A PHE* 3.9 28.7 - - + -
338A CYS* 4.2 3.6 - - - +
339A VAL* 1.3 73.5 - - - +
341A LYS* 1.3 63.4 + - - +
344A HIS* 4.2 19.5 - - + +
346A LEU* 4.0 30.1 - - + +
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Residues in contact with LYS 341 (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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294A VAL* 3.7 7.6 - - - +
297A GLY 4.6 0.4 - - - -
298A GLU* 3.7 26.2 - - - +
339A VAL* 3.6 25.2 + - + +
340A VAL* 1.3 77.5 - - - +
342A GLN* 1.3 68.8 + - - +
343A GLY 3.1 0.5 + - - -
344A HIS* 3.0 41.4 + - + +
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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