Contacts of the strand formed by residues 269 - 275 (chain C) in PDB entry 4GLM
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 269 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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247C TYR* 4.8 16.1 - - + -
248C GLY 3.7 5.2 - - - -
249C VAL* 4.7 10.3 - - + +
267C GLY 3.5 3.7 + - - +
268C ASP* 1.3 71.4 - - - +
270C ILE* 1.3 61.6 + - - +
271C ARG 4.1 1.0 + - - -
284C SER 4.4 1.6 - - - +
285C LEU* 3.4 18.3 - - - +
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Residues in contact with ILE 270 (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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247C TYR* 3.3 6.1 - - - -
248C GLY 2.7 50.1 + - - +
250C ALA* 4.4 0.7 - - + -
262C LEU* 3.8 12.8 - - + -
264C PHE* 3.7 35.7 - - + -
268C ASP 4.3 8.7 - - - +
269C LYS* 1.3 75.3 - - - +
271C ARG* 1.4 72.8 + - - +
272C ILE* 3.5 1.5 + - + +
284C SER 3.6 17.3 - - - +
285C LEU* 4.3 12.8 - - + -
292C PHE* 3.8 28.3 - - + -
297C VAL* 3.9 20.4 - - + -
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Residues in contact with ARG 271 (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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245B LEU* 3.1 44.0 + - - +
246B THR* 2.9 21.1 + - - -
301B PRO* 4.1 17.3 - - + +
246C THR 4.5 9.0 - - - +
247C TYR* 3.7 37.4 + - + -
269C LYS 4.1 0.6 + - - -
270C ILE* 1.4 68.4 - - - +
272C ILE* 1.3 75.1 + - - +
273C LEU* 3.5 16.5 + - + +
283C GLY* 3.0 6.8 - - - -
284C SER* 2.9 45.5 + - - +
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Residues in contact with ILE 272 (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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246B THR* 4.7 0.2 + - - -
246C THR* 2.8 39.9 + - - +
247C TYR 4.0 1.3 - - - -
248C GLY* 3.9 11.2 - - - +
270C ILE* 3.8 12.1 - - + +
271C ARG* 1.3 87.2 + - - +
273C LEU* 1.3 63.1 + - - +
274C ALA 4.1 21.3 - - - +
275C THR* 4.7 6.5 - - + -
281C LEU* 4.1 12.8 - - + -
282C GLU 3.8 2.7 - - - +
292C PHE* 3.7 30.3 - - + -
299C LEU* 3.8 32.5 - - + -
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Residues in contact with LEU 273 (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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246B THR* 3.7 31.2 - - + +
272B ILE* 4.8 2.4 - - - +
275B THR* 4.3 0.7 + - - -
299B LEU* 4.2 27.2 - - + +
301B PRO* 3.7 33.7 - - + -
271C ARG* 3.8 20.2 - - + +
272C ILE* 1.3 74.2 - - - +
274C ALA* 1.3 58.8 + - - +
282C GLU* 2.8 20.9 + - + +
283C GLY* 4.0 21.8 - - - +
284C SER* 4.2 2.9 - - - +
289C THR* 4.1 21.1 - - + -
403C UNX 2.7 24.8 - - - -
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Residues in contact with ALA 274 (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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272B ILE* 6.0 0.2 - - + -
275B THR* 3.4 20.9 - - + +
281B LEU* 4.4 6.1 - - + -
299B LEU* 3.7 21.1 - - + -
272C ILE* 3.8 4.1 - - - +
273C LEU* 1.3 81.2 - - - +
275C THR* 1.3 63.9 + - - +
276C LEU* 4.4 10.3 - - + -
281C LEU* 3.5 5.4 - - - +
282C GLU* 2.8 36.4 + - + +
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Residues in contact with THR 275 (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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275B THR* 2.6 50.1 + - - +
276B LEU 4.0 7.8 + - - +
272C ILE* 4.7 8.7 - - + -
274C ALA* 1.3 72.1 - - - +
276C LEU* 1.3 62.0 + - - +
281C LEU* 3.6 25.1 - - + -
299C LEU* 5.8 5.8 - - + -
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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