Contacts of the strand formed by residues 354 - 361 (chain C) in PDB entry 6T8G
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 VAL 354 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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343C LEU* 4.4 0.4 - - + -
344C GLU* 3.6 51.5 - - + +
347C LEU* 3.8 24.9 - - + -
348C LYS* 4.5 4.9 - - + +
352C VAL* 5.2 2.0 - - + -
353C GLU* 1.3 83.2 - - - +
355C SER* 1.3 62.7 + - - +
356C VAL* 3.8 22.9 - - + -
370C ILE* 3.6 33.0 - - + -
371C GLN 4.4 1.8 - - - -
372C PRO* 4.7 1.8 - - - -
373C ALA* 5.5 0.4 - - - -
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Residues in contact with SER 355 (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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344C GLU* 5.4 1.6 - - - -
354C VAL* 1.3 73.5 - - - +
356C VAL* 1.3 65.1 + - - +
357C ASP* 4.4 0.3 - - - +
371C GLN* 2.3 66.4 + - - +
372C PRO 4.7 2.3 + - - -
373C ALA* 5.5 2.4 - - - -
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Residues in contact with VAL 356 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340C SER* 4.1 33.7 - - - +
341C ARG* 4.1 21.0 + - - +
343C LEU* 4.0 18.4 - - + -
344C GLU* 4.4 9.8 + - + -
354C VAL* 3.8 20.6 + - + -
355C SER* 1.3 72.2 - - - +
357C ASP* 1.3 64.1 + - - +
358C SER 4.8 3.6 - - - +
359C VAL* 5.0 3.8 - - + -
368C PHE* 4.6 15.7 - - + -
369C GLU 3.8 11.2 - - - +
370C ILE* 4.5 4.3 - - + +
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Residues in contact with ASP 357 (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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355C SER 4.5 4.5 - - - +
356C VAL* 1.3 77.3 - - - +
358C SER* 1.3 65.5 + - - +
369C GLU* 2.9 25.5 + - + +
371C GLN* 4.7 11.8 - - + +
408C THR* 4.6 10.7 - - + +
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Residues in contact with SER 358 (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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356C VAL* 4.8 1.5 - - - +
357C ASP* 1.3 84.0 - - - +
359C VAL* 1.3 69.3 + - - +
360C HIS* 4.4 5.8 + - - -
368C PHE* 4.9 0.2 - - - -
369C GLU* 2.4 60.6 + - - +
406C LYS* 4.7 0.9 + - - -
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Residues in contact with VAL 359 (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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336C LEU* 3.7 42.0 - - + +
340C SER* 3.7 13.2 - - - +
356C VAL* 5.0 3.6 - - + -
358C SER* 1.3 82.2 - - - +
360C HIS* 1.3 72.2 + - - +
361C PRO* 3.6 7.7 - - - +
366C THR* 3.7 10.5 - - + -
367C ARG 3.3 13.0 - - - +
368C PHE* 3.6 29.6 - - + -
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Residues in contact with HIS 360 (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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358C SER* 4.4 5.0 + - - -
359C VAL* 1.3 78.8 + - - +
361C PRO* 1.3 67.1 - - - +
362C GLY* 3.7 0.9 + - - -
367C ARG* 2.7 65.7 + - + +
369C GLU* 3.1 32.8 + - + -
406C LYS* 4.2 6.4 + - - -
447C ILE 4.8 4.7 - - - +
448C GLY* 6.0 4.9 - - - -
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Residues in contact with PRO 361 (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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330C SER 5.0 7.4 - - - +
331C TYR* 4.9 21.1 - - + +
336C LEU* 4.6 17.7 - - + -
359C VAL* 3.6 14.1 - - + +
360C HIS* 1.3 84.8 - - - +
362C GLY* 1.3 58.1 + - - +
366C THR* 3.7 17.7 - - + +
447C ILE 4.9 1.0 - - - +
448C GLY* 4.8 6.8 - - - +
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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