Contacts of the strand formed by residues 349 - 357 (chain C) in PDB entry 6GR2
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 GLY 349 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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225C SER* 4.0 7.0 - - - -
227C VAL* 3.5 16.2 - - - -
228C ARG* 4.9 0.7 - - - -
322C CYS* 3.8 7.3 - - - -
325C LEU* 3.3 28.6 - - - +
344C THR 4.7 3.1 - - - +
347C GLY* 3.6 14.0 + - - +
348C PHE* 1.3 74.4 - - - +
350C GLY* 1.3 61.8 + - - -
351C CYS 3.9 0.9 + - - -
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Residues in contact with GLY 350 (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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136C GLY 5.3 1.7 + - - -
137C GLY* 3.6 24.0 - - - -
138C GLY* 4.6 5.4 - - - -
224C ASN* 3.3 4.3 - - - +
225C SER* 2.8 34.8 + - - -
227C VAL 3.3 13.8 + - - -
325C LEU* 4.1 1.5 - - - +
344C THR 5.4 0.9 - - - -
349C GLY* 1.3 73.0 - - - -
351C CYS* 1.3 60.2 + - - -
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Residues in contact with CYS 351 (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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137C GLY 3.1 25.3 + - - +
138C GLY* 5.1 2.5 - - - -
139C LEU* 3.8 24.0 - - + -
222C ILE* 3.8 20.0 - - + -
223C THR 3.0 6.7 - - - +
224C ASN* 3.6 26.9 - - - -
325C LEU* 3.7 13.4 - - - +
343C MET* 3.7 0.5 - - - -
344C THR* 3.3 39.9 + - + +
349C GLY 3.9 1.2 + - - -
350C GLY* 1.3 72.6 - - - -
352C THR* 1.3 61.5 + - - +
379C TYR* 5.5 0.2 - - - -
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Residues in contact with THR 352 (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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221C LEU 3.4 1.7 - - - +
222C ILE* 3.3 3.4 - - - -
223C THR* 2.6 52.2 + - - -
325C LEU* 4.0 12.0 - - - +
328C LEU* 4.1 14.2 - - - +
329C VAL* 3.7 22.9 - - + +
332C ALA* 5.5 0.9 - - + -
341C SER* 2.9 29.4 - - - +
342C ARG 3.4 12.9 + - - +
343C MET* 4.3 0.2 - - - -
344C THR* 4.6 0.2 - - - -
351C CYS* 1.3 77.4 + - - +
353C VAL* 1.3 60.5 + - - +
354C THR* 3.6 6.7 - - - +
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Residues in contact with VAL 353 (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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38C VAL* 3.9 25.1 - - + -
39C ASN 3.8 18.2 - - - +
40C LEU* 4.1 16.8 - - + +
220C VAL* 3.8 26.2 - - + -
221C LEU 3.4 3.8 - - - +
222C ILE* 4.5 2.0 - - + +
307C MET* 3.6 11.2 - - + +
341C SER* 3.3 2.9 - - - -
342C ARG* 3.0 43.8 + - + +
344C THR* 4.3 8.3 - - + +
351C CYS 4.3 0.2 - - - -
352C THR* 1.3 69.9 - - - +
354C THR* 1.3 67.1 + - - +
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Residues in contact with THR 354 (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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219C ALA 3.7 1.0 - - - +
220C VAL* 3.5 3.4 - - - -
221C LEU* 2.7 60.0 + - + +
223C THR* 5.1 2.6 + - - -
307C MET* 4.6 0.7 - - - -
332C ALA* 4.0 10.6 - - + +
338C VAL* 3.5 29.2 - - + -
340C GLY 3.3 15.7 - - - +
341C SER* 2.5 24.5 + - - -
352C THR* 3.6 6.2 - - - +
353C VAL* 1.3 74.7 - - - +
355C LEU* 1.3 63.4 + - - +
356C LEU* 3.9 3.9 + - + +
364C ALA* 6.1 0.7 - - + -
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Residues in contact with LEU 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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40C LEU* 5.8 5.2 - - + -
213C LEU* 4.9 4.7 - - + -
218C LEU* 3.3 42.2 - - + -
219C ALA 3.6 0.7 - - - +
220C VAL* 3.6 28.7 - - + -
295C LEU* 5.0 2.2 - - + -
300C TYR* 4.4 21.1 - - + +
303C PHE* 4.4 26.5 - - + -
307C MET* 4.0 18.5 - - + +
338C VAL* 3.5 1.4 - - - +
339C TYR* 2.6 44.4 + - + -
340C GLY 3.0 10.2 + - - +
353C VAL* 6.6 0.2 - - + -
354C THR* 1.3 70.0 - - - +
356C LEU* 1.3 55.3 + - - +
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Residues in contact with LEU 356 (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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218C LEU* 3.5 4.9 - - - +
219C ALA* 2.9 36.6 + - + +
221C LEU* 5.8 4.3 - - + -
337C GLY 3.3 11.9 - - - +
338C VAL* 3.7 21.8 - - + -
339C TYR* 3.9 7.4 - - - -
354C THR* 4.4 7.6 - - + +
355C LEU* 1.3 77.7 - - - +
357C GLU* 1.3 66.7 + - - +
360C ALA* 5.0 3.4 - - + -
361C ALA* 5.6 3.4 - - + +
364C ALA* 5.5 4.9 - - + -
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Residues in contact with GLU 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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217C LYS 3.6 9.2 - - - +
219C ALA* 4.6 0.4 - - - +
336C PRO 4.7 0.5 - - - +
337C GLY* 2.7 39.0 + - - +
339C TYR* 3.9 23.5 + - + +
356C LEU* 1.3 74.2 - - - +
358C ALA* 1.3 60.6 + - - +
359C SER* 4.2 13.3 + - - +
360C ALA* 2.8 33.7 + - + +
361C ALA* 3.5 4.3 + - - +
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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