Contacts of the helix formed by residues 303 - 310 (chain C) in PDB entry 3F98
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 303 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219C ASN* 3.5 15.5 - - - +
281C GLN* 5.0 0.2 + - - -
302C LEU* 1.3 75.3 - - - +
304C ASP* 1.3 66.2 + - - -
305C GLU* 3.1 22.4 + - - -
306C VAL* 3.3 21.0 + - - +
307C TYR* 4.0 6.9 - - - -
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Residues in contact with ASP 304 (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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302C LEU 4.9 1.6 - - - +
303C GLY* 1.3 72.9 - - - -
305C GLU* 1.3 64.1 + - - +
306C VAL 3.2 1.3 + - - -
307C TYR* 3.3 23.5 + - + +
308C SER* 5.1 1.0 + - - -
330C LYS* 4.6 6.8 + - - -
333C LYS* 2.8 40.1 + - - +
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Residues in contact with GLU 305 (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 ASN* 4.9 0.5 + - - -
223C ARG* 3.0 30.1 + - - +
281C GLN* 4.7 3.3 + - - +
303C GLY* 3.2 23.4 + - - -
304C ASP* 1.3 79.7 + - - +
306C VAL* 1.3 77.4 + - + +
307C TYR 3.4 0.7 + - - -
308C SER* 3.8 8.7 + - - -
309C ARG* 3.3 51.5 + - - +
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Residues in contact with VAL 306 (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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280C ILE* 3.6 26.2 - - + +
281C GLN* 3.5 26.7 - - - +
284C SER* 3.2 31.2 - - - +
302C LEU* 4.5 6.7 - - + -
303C GLY 3.3 19.5 - - - +
304C ASP 3.2 1.4 - - - -
305C GLU* 1.3 94.1 - - + +
307C TYR* 1.3 67.7 + - + +
309C ARG* 3.0 20.0 + - - +
310C ILE* 3.4 13.7 - - + +
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Residues in contact with TYR 307 (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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280C ILE* 5.0 4.3 - - + -
299C MET* 4.0 10.7 - - + +
302C LEU* 4.2 21.1 + - + +
303C GLY 4.0 6.1 - - - -
304C ASP* 3.3 42.6 - - - +
305C GLU 3.4 1.4 - - - -
306C VAL* 1.3 78.4 - - + +
308C SER* 1.3 60.2 + - - +
309C ARG 3.1 1.6 + - - -
310C ILE* 3.5 15.5 + - - +
330C LYS* 3.7 36.4 + - - +
333C LYS* 3.7 43.0 + - + +
334C CYS* 3.4 37.5 - - - +
339C LYS* 3.8 13.9 - - - +
341C ARG* 4.8 1.6 + - - -
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Residues in contact with SER 308 (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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304C ASP 5.1 0.8 + - - -
305C GLU* 3.8 11.3 + - - -
307C TYR* 1.3 76.7 - - - +
309C ARG* 1.3 64.4 + - - +
310C ILE 3.4 2.3 + - - -
311C PRO* 5.4 0.5 - - - +
339C LYS* 4.4 17.1 + - - +
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Residues in contact with ARG 309 (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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284C SER* 3.6 32.3 + - - +
287C GLN* 4.1 4.7 + - - -
305C GLU* 3.3 48.8 + - - +
306C VAL* 3.0 12.0 + - - +
308C SER* 1.3 84.9 + - - +
310C ILE* 1.3 58.3 + - - +
311C PRO* 3.2 13.8 - - - +
583C FMT 3.3 38.6 + - - +
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Residues in contact with ILE 310 (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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280C ILE* 3.4 42.0 - - + +
283C LEU* 3.8 18.6 - - + -
284C SER* 3.7 15.0 - - - +
306C VAL* 3.4 22.9 - - + +
307C TYR* 3.5 10.8 + - + +
308C SER 3.4 3.2 - - - -
309C ARG* 1.3 80.5 - - - +
311C PRO* 1.3 59.6 - - - +
312C GLN* 3.6 23.1 - - - +
314C LEU* 5.2 5.2 - - + -
334C CYS* 5.4 1.8 - - - -
339C LYS* 3.6 12.1 - - - +
341C ARG* 2.8 35.9 + - - +
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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