Contacts of the helix formed by residues 314 - 318 (chain C) in PDB entry 5TXV
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 314 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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437B ASP* 4.0 26.3 + - - +
440B ARG* 3.3 33.6 - - + +
441B PHE* 3.8 23.3 - - + -
262C CYS* 4.1 3.3 - - - -
310C PHE* 3.5 7.3 - - - +
313C ALA* 1.3 79.7 - - - +
315C PRO* 1.3 69.8 - - + +
316C SER* 3.1 13.2 - - - +
317C ASP* 2.8 34.5 + - - +
318C LEU 4.0 1.0 + - - -
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Residues in contact with PRO 315 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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440B ARG 2.8 30.3 - - - +
441B PHE* 3.5 20.9 - - + +
54C LEU* 3.6 31.9 - - + -
56C ILE* 3.8 6.5 - - + -
310C PHE* 3.4 21.3 - - + -
314C LYS* 1.3 86.5 - - + +
316C SER* 1.3 59.4 + - - -
318C LEU* 3.1 28.6 + - + +
323C GLN* 3.4 8.3 - - - +
329C ARG* 3.9 8.3 - - - +
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Residues in contact with SER 316 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387B THR* 4.4 3.8 - - - -
388B GLU* 3.0 38.0 + - - +
394B ARG* 5.7 1.1 - - - -
440B ARG* 3.1 45.4 + - - +
263C LYS* 5.4 0.7 - - - -
314C LYS* 3.8 4.7 - - - +
315C PRO* 1.3 78.2 - - - +
317C ASP* 1.3 63.4 + - - +
318C LEU 3.3 1.2 - - - +
323C GLN* 2.5 30.8 + - - +
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Residues in contact with ASP 317 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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388B GLU* 5.2 5.0 - - - +
262C CYS* 3.9 17.6 - - + -
263C LYS* 3.7 51.0 + - + +
275C GLU* 4.4 4.2 - - - +
278C GLN* 4.5 2.1 + - - -
313C ALA* 3.4 11.3 - - - +
314C LYS* 2.8 35.6 + - - +
316C SER* 1.3 78.7 + - - +
318C LEU* 1.3 65.4 + - - +
319C ILE 3.8 0.3 + - - -
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Residues in contact with LEU 318 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54C LEU* 4.6 5.2 - - + -
258C ILE* 4.3 19.7 - - + +
261C ILE* 5.2 0.4 - - + -
262C CYS* 3.5 23.1 - - - -
278C GLN* 3.4 19.5 - - - +
310C PHE* 4.7 5.6 - - + -
315C PRO* 3.1 32.0 + - + +
316C SER 3.3 1.0 - - - +
317C ASP* 1.3 81.8 - - - +
319C ILE* 1.3 62.3 + - - +
320C PRO* 3.5 1.6 - - - +
322C LEU* 3.7 16.6 - - + -
323C GLN* 2.6 37.4 + - + -
326C LEU* 4.3 24.2 - - + -
329C ARG* 5.8 0.9 - - - +
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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