Contacts of the strand formed by residues 274 - 279 (chain C) in PDB entry 4HH3
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 274 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242B ARG* 6.1 0.2 - - - -
272C SER* 3.3 10.7 + - - -
273C VAL* 1.3 81.1 - - - +
275C ALA* 1.3 58.8 + - - -
302C TRP* 3.3 20.4 - - - -
303C SER* 3.0 24.7 + - - -
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Residues in contact with ALA 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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242B ARG* 3.6 43.5 - - - +
274C GLY* 1.3 73.5 - - - -
276C VAL* 1.3 62.6 + - - +
302C TRP* 3.7 9.1 - - - -
303C SER* 3.3 8.7 - - - +
323C ARG 5.0 0.2 - - - +
324C THR* 3.7 19.4 - - + +
325C SER 4.6 2.1 + - - -
326C THR* 3.8 10.2 + - - -
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Residues in contact with VAL 276 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275C ALA* 1.3 76.6 - - - +
277C LEU* 1.3 66.3 + - - +
297C LEU* 3.7 20.4 - - + -
302C TRP* 3.8 21.3 - - + -
303C SER 2.9 5.8 + - - +
304C THR* 3.3 26.2 - - + +
305C SER* 3.1 23.9 + - - +
324C THR* 3.6 5.3 + - - -
326C THR* 3.5 22.9 - - + +
328C VAL* 3.7 29.4 - - + -
394C LEU* 4.6 2.2 - - + -
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Residues in contact with LEU 277 (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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276C VAL* 1.3 76.0 - - - +
278C VAL* 1.3 66.6 + - - +
305C SER* 3.4 23.1 - - - +
307C VAL* 3.5 28.7 - - + -
315C LEU* 3.7 13.2 - - + -
318C ARG* 3.9 31.6 - - + -
319C LEU* 4.1 18.4 - - + +
322C SER* 4.2 11.0 - - - +
324C THR* 3.9 11.4 - - + -
326C THR 3.0 8.9 + - - +
327C LEU* 3.5 16.8 - - + +
328C VAL* 2.9 24.9 + - - +
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Residues in contact with VAL 278 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276C VAL* 4.9 0.2 - - + -
277C LEU* 1.3 76.7 - - - +
279C ALA* 1.3 62.6 + - - +
290C ALA* 3.8 34.3 - - + +
293C ALA* 4.0 22.0 - - + -
294C ALA* 4.4 4.5 - - - +
297C LEU* 4.2 10.8 - - + -
304C THR* 4.0 22.0 - - + -
305C SER 2.8 10.5 + - - +
306C VAL* 3.3 9.7 - - + +
307C VAL 2.9 24.6 + - - +
328C VAL* 3.3 19.5 - - + +
330C ALA* 4.1 8.5 - - + -
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Residues in contact with ALA 279 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277C LEU 4.0 0.2 + - - -
278C VAL* 1.3 76.1 - - - +
280C GLY* 1.3 67.4 + - - +
290C ALA* 5.5 0.7 - - - -
307C VAL* 3.1 24.7 - - + +
309C PRO* 4.4 1.1 - - + -
315C LEU* 3.9 13.9 - - + -
327C LEU* 3.8 20.9 - - + -
328C VAL 2.8 7.3 + - - -
329C VAL* 3.4 7.9 - - - +
330C ALA* 2.9 27.3 + - - -
346C PHE* 5.2 2.0 - - + -
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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