Contacts of the helix formed by residues 287 - 293 (chain A) in PDB entry 3SRG
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 ASN 287 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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29A ASN 3.5 12.4 + - - +
30A VAL 3.1 22.4 + - - -
31A HIS 4.1 0.2 - - - -
32A ARG 3.0 27.5 + - - +
285A HIS* 4.4 4.0 - - - +
286A PRO* 1.3 82.3 - - + +
288A GLY* 1.3 62.1 + - - +
289A MET* 2.9 27.4 + - - +
290A ARG* 3.3 45.6 + - + +
291A ILE* 3.6 12.3 + - - +
300A PRO* 5.2 1.6 - - - +
301A GLY 6.1 0.4 - - - +
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Residues in contact with GLY 288 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28A PHE* 2.8 24.5 + - - -
267A LEU* 3.5 31.5 - - - +
287A ASN* 1.3 71.1 - - - +
289A MET* 1.3 67.6 + - - +
291A ILE* 3.3 5.7 + - - +
292A PHE* 2.9 30.3 + - - +
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Residues in contact with MET 289 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A PHE* 3.2 42.2 - - + -
28A PHE* 3.3 8.6 + - + +
30A VAL* 3.8 23.3 - - + +
287A ASN* 2.9 12.6 + - - +
288A GLY* 1.3 75.6 - - - +
290A ARG* 1.3 62.2 + - + +
293A PHE* 2.9 58.3 + - + +
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Residues in contact with ARG 290 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32A ARG 3.5 11.9 + - - -
33A GLU* 2.7 46.2 + - - +
34A VAL* 5.3 7.5 - - - +
287A ASN* 3.3 34.9 + - + +
288A GLY 3.1 0.6 - - - -
289A MET* 1.3 83.3 - - + +
291A ILE* 1.3 59.6 + - - +
293A PHE 3.8 13.4 - - - +
294A TYR* 4.0 7.3 - - - -
298A ASN* 3.0 47.0 + - - +
299A PRO 3.4 19.0 + - - -
300A PRO* 3.7 30.6 - - + +
301A GLY 5.2 0.2 - - - +
324A ASN* 5.7 5.5 + - - +
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Residues in contact with ILE 291 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74A ILE* 3.8 12.7 - - + +
75A MET 5.7 0.5 + - - -
267A LEU* 4.6 0.7 - - + -
285A HIS* 3.6 28.7 - - + +
287A ASN 3.6 5.3 + - - +
288A GLY* 3.3 23.1 - - - +
290A ARG* 1.3 80.7 - - - +
292A PHE* 1.3 75.7 + - + +
293A PHE 3.5 0.2 - - - -
294A TYR* 4.8 3.6 + - - +
300A PRO* 3.7 22.4 - - + -
330A GLY* 3.8 11.2 - - - -
346A VAL* 3.8 15.9 - - + -
347A PHE* 3.7 30.8 - - + -
1358A OCH 3.7 20.2 - - + -
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Residues in contact with PHE 292 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28A PHE* 3.7 12.1 - + + -
71A TYR* 5.8 2.5 - + - -
73A GLY 3.6 19.8 - - - +
74A ILE* 3.9 12.5 - - + +
196A MET* 3.5 36.3 - - + -
222A PHE* 3.9 16.2 - + - -
240A LEU* 3.7 24.9 - - + -
241A LEU* 3.9 15.5 - - + -
267A LEU* 4.1 4.7 - - + -
288A GLY 2.9 24.5 + - - +
291A ILE* 1.3 86.6 - - + +
293A PHE* 1.3 83.0 + - + +
294A TYR 3.8 1.2 + - - -
1358A OCH 3.6 32.1 - + - -
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Residues in contact with PHE 293 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A PHE* 4.3 9.2 - + - -
28A PHE* 5.1 3.8 - + - -
196A MET* 5.8 0.9 - - + -
197A HIS* 4.2 26.9 - + - -
289A MET* 2.9 60.1 + - + +
290A ARG* 3.8 6.1 - - - +
292A PHE* 1.3 96.8 - - + +
294A TYR* 1.3 68.5 + - - +
295A ASP* 3.3 6.9 + - - +
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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