Contacts of the helix formed by residues 313 - 320 (chain B) in PDB entry 1U5U
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 SER 313 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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311B PRO 3.9 1.8 + - - -
312B LEU* 1.3 78.4 - - - +
314B PRO* 1.3 72.8 - - - +
315B ASP* 3.7 10.2 + - - +
316B VAL* 3.1 24.3 + - - +
317B LEU* 2.7 30.7 + - - +
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Residues in contact with PRO 314 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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312B LEU 3.5 4.4 - - - +
313B SER* 1.3 89.2 - - - +
315B ASP* 1.3 66.3 - - - +
317B LEU* 3.7 9.0 - - + +
318B GLU* 2.9 29.9 + - - +
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Residues in contact with ASP 315 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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313B SER* 3.2 6.5 + - - +
314B PRO* 1.3 83.7 - - - +
316B VAL* 1.3 66.4 + - + +
318B GLU* 3.5 9.2 + - - +
319B LYS* 3.1 27.0 + - - +
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Residues in contact with VAL 316 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100B ARG* 3.4 33.7 - - - +
127B ASP* 3.8 6.3 - - - +
312B LEU* 4.0 14.6 - - + -
313B SER* 3.1 25.6 + - - +
315B ASP* 1.3 75.4 - - + +
317B LEU* 1.3 65.5 + - - +
319B LYS* 3.3 20.0 + - - +
320B THR* 2.9 26.0 + - - -
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Residues in contact with LEU 317 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64B ARG* 2.9 21.3 + - - -
70B GLY 3.9 7.4 - - - +
71B THR* 3.5 34.8 - - - +
72B GLY* 3.8 14.1 - - - +
101B LEU 4.0 1.3 - - - +
102B ARG* 3.7 39.5 - - + +
312B LEU* 3.7 32.6 - - + +
313B SER 2.7 22.7 + - - +
314B PRO* 3.7 7.2 - - + +
316B VAL* 1.3 72.9 - - - +
318B GLU* 1.3 60.5 + - - +
320B THR* 3.2 12.2 + - - +
322B PHE* 5.9 0.4 - - + -
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Residues in contact with GLU 318 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62B PHE 4.8 1.0 - - - +
63B ARG* 2.7 64.7 + - + +
64B ARG* 2.9 32.4 + - - +
68B THR 4.3 0.3 - - - +
102B ARG* 4.6 1.6 + - - -
314B PRO 2.9 19.3 + - - +
315B ASP* 3.6 12.1 - - - +
317B LEU* 1.3 79.5 - - - +
319B LYS* 1.3 57.8 + - - +
360B ARG* 2.9 24.7 + - - +
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Residues in contact with LYS 319 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127B ASP* 3.0 46.2 + - + +
128B SER* 4.8 2.3 + - - -
315B ASP 3.1 13.3 + - - +
316B VAL* 3.3 30.4 - - - +
318B GLU* 1.3 73.5 - - - +
320B THR* 1.3 66.4 + - - +
321B ALA* 3.6 4.9 + - - +
360B ARG* 4.3 6.9 + - - +
361B LYS* 5.9 1.7 - - - -
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Residues in contact with THR 320 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64B ARG* 2.8 23.4 + - - -
100B ARG* 2.9 26.8 + - + -
122B LYS* 4.0 13.5 - - - -
126B SER 4.1 5.4 - - - +
127B ASP* 3.2 13.7 - - - +
312B LEU* 4.3 3.1 - - + +
316B VAL 2.9 19.3 + - - -
317B LEU* 3.2 15.1 + - - -
319B LYS* 1.3 78.5 - - - +
321B ALA* 1.3 62.1 + - - +
322B PHE* 3.6 32.1 + - + -
360B ARG* 3.3 8.1 + - - -
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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