Contacts of the helix formed by residues 330 - 337 (chain C) in PDB entry 6TXC
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 ASP 330 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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119A ASN* 4.9 0.2 + - - -
125A HIS* 3.0 27.9 + - + -
324B GLY 4.6 8.3 - - - +
328C ASN 4.3 1.0 + - - +
329C PHE* 1.3 81.3 - - - +
331C TYR* 1.3 62.2 + - - +
332C LYS* 3.3 23.9 + - - +
333C ARG* 3.4 21.6 + - + +
334C PHE* 3.4 16.6 + - - +
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Residues in contact with TYR 331 (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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122C ILE* 6.0 0.9 - - + -
123C HIS* 3.6 21.0 + + - +
173C TYR* 4.4 6.9 + - - -
174C LEU* 3.4 31.4 - - + +
177C CYS* 5.6 3.3 - - + -
313C TRP* 3.7 49.9 - + + -
317C ALA* 5.6 6.3 - - + -
329C PHE* 3.7 18.7 + - + -
330C ASP* 1.3 71.1 + - - +
332C LYS* 1.3 104.2 + - + +
334C PHE* 3.0 6.6 + - - +
335C ILE* 3.0 42.2 + - + +
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Residues in contact with LYS 332 (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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123A HIS 5.3 6.5 + - - -
124A GLY* 5.9 6.1 - - - -
125A HIS* 5.1 9.4 - - + +
332A LYS* 4.6 15.6 - - - +
330C ASP* 3.3 11.5 + - - +
331C TYR* 1.3 118.6 - - + +
333C ARG* 1.3 61.8 + - - +
335C ILE* 3.5 7.9 + - - +
336C LYS* 3.2 30.3 + - - +
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Residues in contact with ARG 333 (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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117A VAL* 5.5 0.6 - - - +
119A ASN* 5.4 4.0 - - - +
125A HIS* 3.2 56.5 + - + +
330C ASP* 3.4 19.4 + - - +
331C TYR 3.2 0.6 - - - -
332C LYS* 1.3 77.1 - - - +
334C PHE* 1.3 64.6 + - - +
336C LYS* 3.2 4.2 + - - +
337C PHE* 3.1 38.0 + - + -
354C LYS* 3.5 19.0 - - - +
355C GLU* 2.7 39.4 + - - +
358C ASN* 3.7 12.3 - - - +
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Residues in contact with PHE 334 (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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178C LEU* 5.3 3.8 - - + -
308C ILE* 4.0 15.9 - - + -
313C TRP* 3.3 36.6 - + + -
329C PHE* 4.6 8.7 - + + -
330C ASP 3.4 9.0 + - - +
331C TYR* 3.0 13.0 + - - +
333C ARG* 1.3 79.2 - - - +
335C ILE* 1.3 62.0 + - - +
337C PHE* 3.1 8.1 + - + +
338C ALA* 3.0 31.5 + - + +
349C ILE* 4.6 18.4 - - + -
351C ALA* 3.8 26.9 - - + -
355C GLU* 5.5 8.7 - - + -
359C LEU* 3.7 33.2 - - + -
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Residues in contact with ILE 335 (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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174C LEU* 5.1 2.0 - - + +
177C CYS* 4.3 22.4 - - + +
178C LEU* 4.1 19.0 - - + +
181C ALA* 3.8 28.8 - - + +
182C LEU* 5.9 0.2 - - - +
313C TRP* 3.8 20.6 - - + -
331C TYR* 3.0 41.2 + - + +
332C LYS* 3.6 9.0 - - - +
334C PHE* 1.3 77.0 - - - +
336C LYS* 1.3 67.4 + - + +
337C PHE 3.3 0.5 + - - -
338C ALA* 3.3 19.8 + - - +
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Residues in contact with LYS 336 (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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115A MET* 4.6 11.4 - - - +
117A VAL* 4.6 15.0 - - + -
125A HIS* 3.7 37.3 + - + +
126A ILE* 5.0 0.4 - - - +
127A GLU* 3.5 43.8 + - + +
173A TYR* 6.3 0.8 - - - -
332C LYS* 3.2 17.9 + - - +
333C ARG* 3.2 9.8 + - - +
335C ILE* 1.3 81.5 - - + +
337C PHE* 1.3 68.8 + - + +
338C ALA 3.4 3.7 + - - +
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Residues in contact with PHE 337 (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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115A MET* 5.9 0.9 - - + -
117A VAL* 4.1 35.7 - - + -
333C ARG* 3.1 54.1 + - + +
334C PHE* 3.1 9.7 + - + +
336C LYS* 1.3 79.5 - - + +
338C ALA* 1.3 59.0 + - - +
339C ARG* 5.2 1.0 - - - +
350C CYS 3.9 0.3 - - - +
351C ALA* 3.7 5.7 - - - +
352C ARG* 3.4 45.6 + - + +
354C LYS* 3.6 26.7 - - - -
355C GLU* 3.8 30.5 - - + -
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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